diff --git a/api/core/rag/datasource/keyword/jieba/jieba.py b/api/core/rag/datasource/keyword/jieba/jieba.py
index b07dc108be..b8d5db7a43 100644
--- a/api/core/rag/datasource/keyword/jieba/jieba.py
+++ b/api/core/rag/datasource/keyword/jieba/jieba.py
@@ -97,13 +97,13 @@ class Jieba(BaseKeyword):
 
         documents = []
 
-        segment_query_stmt = db.session.query(DocumentSegment).where(
+        segment_query_stmt = select(DocumentSegment).where(
             DocumentSegment.dataset_id == self.dataset.id, DocumentSegment.index_node_id.in_(sorted_chunk_indices)
         )
         if document_ids_filter:
             segment_query_stmt = segment_query_stmt.where(DocumentSegment.document_id.in_(document_ids_filter))
 
-        segments = db.session.execute(segment_query_stmt).scalars().all()
+        segments = db.session.scalars(segment_query_stmt).all()
         segment_map = {segment.index_node_id: segment for segment in segments}
         for chunk_index in sorted_chunk_indices:
             segment = segment_map.get(chunk_index)
diff --git a/api/core/rag/datasource/retrieval_service.py b/api/core/rag/datasource/retrieval_service.py
index cc6ec12c75..203a8588d6 100644
--- a/api/core/rag/datasource/retrieval_service.py
+++ b/api/core/rag/datasource/retrieval_service.py
@@ -432,10 +432,11 @@ class RetrievalService:
             # Batch query dataset documents
             dataset_documents = {
                 doc.id: doc
-                for doc in db.session.query(DatasetDocument)
-                .where(DatasetDocument.id.in_(document_ids))
-                .options(load_only(DatasetDocument.id, DatasetDocument.doc_form, DatasetDocument.dataset_id))
-                .all()
+                for doc in db.session.scalars(
+                    select(DatasetDocument)
+                    .where(DatasetDocument.id.in_(document_ids))
+                    .options(load_only(DatasetDocument.id, DatasetDocument.doc_form, DatasetDocument.dataset_id))
+                ).all()
             }
 
             valid_dataset_documents = {}
diff --git a/api/core/rag/datasource/vdb/tidb_on_qdrant/tidb_on_qdrant_vector.py b/api/core/rag/datasource/vdb/tidb_on_qdrant/tidb_on_qdrant_vector.py
index 3c1d5e015f..69c81d521c 100644
--- a/api/core/rag/datasource/vdb/tidb_on_qdrant/tidb_on_qdrant_vector.py
+++ b/api/core/rag/datasource/vdb/tidb_on_qdrant/tidb_on_qdrant_vector.py
@@ -426,11 +426,10 @@ class TidbOnQdrantVectorFactory(AbstractVectorFactory):
                     TIDB_ON_QDRANT_API_KEY = f"{tidb_auth_binding.account}:{tidb_auth_binding.password}"
 
                 else:
-                    idle_tidb_auth_binding = (
-                        db.session.query(TidbAuthBinding)
+                    idle_tidb_auth_binding = db.session.scalar(
+                        select(TidbAuthBinding)
                         .where(TidbAuthBinding.active == False, TidbAuthBinding.status == "ACTIVE")
                         .limit(1)
-                        .one_or_none()
                     )
                     if idle_tidb_auth_binding:
                         idle_tidb_auth_binding.active = True
diff --git a/api/core/rag/datasource/vdb/vector_factory.py b/api/core/rag/datasource/vdb/vector_factory.py
index 5a8d3a2f3f..26531eab88 100644
--- a/api/core/rag/datasource/vdb/vector_factory.py
+++ b/api/core/rag/datasource/vdb/vector_factory.py
@@ -277,7 +277,7 @@ class Vector:
         return self._vector_processor.search_by_vector(query_vector, **kwargs)
 
     def search_by_file(self, file_id: str, **kwargs: Any) -> list[Document]:
-        upload_file: UploadFile | None = db.session.query(UploadFile).where(UploadFile.id == file_id).first()
+        upload_file: UploadFile | None = db.session.get(UploadFile, file_id)
 
         if not upload_file:
             return []
diff --git a/api/core/rag/docstore/dataset_docstore.py b/api/core/rag/docstore/dataset_docstore.py
index e5b794f80d..40f45953af 100644
--- a/api/core/rag/docstore/dataset_docstore.py
+++ b/api/core/rag/docstore/dataset_docstore.py
@@ -4,7 +4,7 @@ from collections.abc import Sequence
 from typing import Any
 
 from graphon.model_runtime.entities.model_entities import ModelType
-from sqlalchemy import func, select
+from sqlalchemy import delete, func, select
 
 from core.model_manager import ModelManager
 from core.rag.index_processor.constant.index_type import IndexTechniqueType
@@ -63,10 +63,8 @@ class DatasetDocumentStore:
         return output
 
     def add_documents(self, docs: Sequence[Document], allow_update: bool = True, save_child: bool = False):
-        max_position = (
-            db.session.query(func.max(DocumentSegment.position))
-            .where(DocumentSegment.document_id == self._document_id)
-            .scalar()
+        max_position = db.session.scalar(
+            select(func.max(DocumentSegment.position)).where(DocumentSegment.document_id == self._document_id)
         )
 
         if max_position is None:
@@ -155,12 +153,14 @@ class DatasetDocumentStore:
                 )
                 if save_child and doc.children:
                     # delete the existing child chunks
-                    db.session.query(ChildChunk).where(
-                        ChildChunk.tenant_id == self._dataset.tenant_id,
-                        ChildChunk.dataset_id == self._dataset.id,
-                        ChildChunk.document_id == self._document_id,
-                        ChildChunk.segment_id == segment_document.id,
-                    ).delete()
+                    db.session.execute(
+                        delete(ChildChunk).where(
+                            ChildChunk.tenant_id == self._dataset.tenant_id,
+                            ChildChunk.dataset_id == self._dataset.id,
+                            ChildChunk.document_id == self._document_id,
+                            ChildChunk.segment_id == segment_document.id,
+                        )
+                    )
                     # add new child chunks
                     for position, child in enumerate(doc.children, start=1):
                         child_segment = ChildChunk(
diff --git a/api/core/rag/embedding/cached_embedding.py b/api/core/rag/embedding/cached_embedding.py
index 3bdad00712..8d1c0da392 100644
--- a/api/core/rag/embedding/cached_embedding.py
+++ b/api/core/rag/embedding/cached_embedding.py
@@ -6,6 +6,7 @@ from typing import Any, cast
 import numpy as np
 from graphon.model_runtime.entities.model_entities import ModelPropertyKey
 from graphon.model_runtime.model_providers.__base.text_embedding_model import TextEmbeddingModel
+from sqlalchemy import select
 from sqlalchemy.exc import IntegrityError
 
 from configs import dify_config
@@ -31,14 +32,14 @@ class CacheEmbedding(Embeddings):
         embedding_queue_indices = []
         for i, text in enumerate(texts):
             hash = helper.generate_text_hash(text)
-            embedding = (
-                db.session.query(Embedding)
-                .filter_by(
-                    model_name=self._model_instance.model_name,
-                    hash=hash,
-                    provider_name=self._model_instance.provider,
+            embedding = db.session.scalar(
+                select(Embedding)
+                .where(
+                    Embedding.model_name == self._model_instance.model_name,
+                    Embedding.hash == hash,
+                    Embedding.provider_name == self._model_instance.provider,
                 )
-                .first()
+                .limit(1)
             )
             if embedding:
                 text_embeddings[i] = embedding.get_embedding()
@@ -112,14 +113,14 @@ class CacheEmbedding(Embeddings):
         embedding_queue_indices = []
         for i, multimodel_document in enumerate(multimodel_documents):
             file_id = multimodel_document["file_id"]
-            embedding = (
-                db.session.query(Embedding)
-                .filter_by(
-                    model_name=self._model_instance.model_name,
-                    hash=file_id,
-                    provider_name=self._model_instance.provider,
+            embedding = db.session.scalar(
+                select(Embedding)
+                .where(
+                    Embedding.model_name == self._model_instance.model_name,
+                    Embedding.hash == file_id,
+                    Embedding.provider_name == self._model_instance.provider,
                 )
-                .first()
+                .limit(1)
             )
             if embedding:
                 multimodel_embeddings[i] = embedding.get_embedding()
diff --git a/api/core/rag/extractor/notion_extractor.py b/api/core/rag/extractor/notion_extractor.py
index 372af8fd94..aa36160711 100644
--- a/api/core/rag/extractor/notion_extractor.py
+++ b/api/core/rag/extractor/notion_extractor.py
@@ -4,6 +4,7 @@ import operator
 from typing import Any, cast
 
 import httpx
+from sqlalchemy import update
 
 from configs import dify_config
 from core.rag.extractor.extractor_base import BaseExtractor
@@ -346,9 +347,11 @@ class NotionExtractor(BaseExtractor):
         if data_source_info:
             data_source_info["last_edited_time"] = last_edited_time
 
-        db.session.query(DocumentModel).filter_by(id=document_model.id).update(
-            {DocumentModel.data_source_info: json.dumps(data_source_info)}
-        )  # type: ignore
+        db.session.execute(
+            update(DocumentModel)
+            .where(DocumentModel.id == document_model.id)
+            .values(data_source_info=json.dumps(data_source_info))
+        )
         db.session.commit()
 
     def get_notion_last_edited_time(self) -> str:
diff --git a/api/core/rag/index_processor/index_processor_base.py b/api/core/rag/index_processor/index_processor_base.py
index a435dfc46a..7d504fdb35 100644
--- a/api/core/rag/index_processor/index_processor_base.py
+++ b/api/core/rag/index_processor/index_processor_base.py
@@ -11,6 +11,7 @@ from typing import TYPE_CHECKING, Any, NotRequired, Optional
 from urllib.parse import unquote, urlparse
 
 import httpx
+from sqlalchemy import select
 from typing_extensions import TypedDict
 
 from configs import dify_config
@@ -200,7 +201,7 @@ class BaseIndexProcessor(ABC):
 
         # Get unique IDs for database query
         unique_upload_file_ids = list(set(upload_file_id_list))
-        upload_files = db.session.query(UploadFile).where(UploadFile.id.in_(unique_upload_file_ids)).all()
+        upload_files = db.session.scalars(select(UploadFile).where(UploadFile.id.in_(unique_upload_file_ids))).all()
 
         # Create a mapping from ID to UploadFile for quick lookup
         upload_file_map = {upload_file.id: upload_file for upload_file in upload_files}
@@ -312,7 +313,7 @@ class BaseIndexProcessor(ABC):
         """
         from services.file_service import FileService
 
-        tool_file = db.session.query(ToolFile).where(ToolFile.id == tool_file_id).first()
+        tool_file = db.session.get(ToolFile, tool_file_id)
         if not tool_file:
             return None
         blob = storage.load_once(tool_file.file_key)
diff --git a/api/core/rag/index_processor/processor/paragraph_index_processor.py b/api/core/rag/index_processor/processor/paragraph_index_processor.py
index 5c10ffbf2d..22ab492cbf 100644
--- a/api/core/rag/index_processor/processor/paragraph_index_processor.py
+++ b/api/core/rag/index_processor/processor/paragraph_index_processor.py
@@ -18,6 +18,7 @@ from graphon.model_runtime.entities.message_entities import (
     UserPromptMessage,
 )
 from graphon.model_runtime.entities.model_entities import ModelFeature, ModelType
+from sqlalchemy import select
 
 from core.app.file_access import DatabaseFileAccessController
 from core.app.llm import deduct_llm_quota
@@ -145,14 +146,12 @@ class ParagraphIndexProcessor(BaseIndexProcessor):
         if delete_summaries:
             if node_ids:
                 # Find segments by index_node_id
-                segments = (
-                    db.session.query(DocumentSegment)
-                    .filter(
+                segments = db.session.scalars(
+                    select(DocumentSegment).where(
                         DocumentSegment.dataset_id == dataset.id,
                         DocumentSegment.index_node_id.in_(node_ids),
                     )
-                    .all()
-                )
+                ).all()
                 segment_ids = [segment.id for segment in segments]
                 if segment_ids:
                     SummaryIndexService.delete_summaries_for_segments(dataset, segment_ids)
@@ -537,11 +536,9 @@ class ParagraphIndexProcessor(BaseIndexProcessor):
 
         # Get unique IDs for database query
         unique_upload_file_ids = list(set(upload_file_id_list))
-        upload_files = (
-            db.session.query(UploadFile)
-            .where(UploadFile.id.in_(unique_upload_file_ids), UploadFile.tenant_id == tenant_id)
-            .all()
-        )
+        upload_files = db.session.scalars(
+            select(UploadFile).where(UploadFile.id.in_(unique_upload_file_ids), UploadFile.tenant_id == tenant_id)
+        ).all()
 
         # Create File objects from UploadFile records
         file_objects = []
diff --git a/api/core/rag/index_processor/processor/parent_child_index_processor.py b/api/core/rag/index_processor/processor/parent_child_index_processor.py
index 70504e6e50..1c5e02e9c8 100644
--- a/api/core/rag/index_processor/processor/parent_child_index_processor.py
+++ b/api/core/rag/index_processor/processor/parent_child_index_processor.py
@@ -6,6 +6,8 @@ import uuid
 from collections.abc import Mapping
 from typing import Any
 
+from sqlalchemy import delete, select
+
 from configs import dify_config
 from core.db.session_factory import session_factory
 from core.entities.knowledge_entities import PreviewDetail
@@ -177,17 +179,16 @@ class ParentChildIndexProcessor(BaseIndexProcessor):
                     child_node_ids = precomputed_child_node_ids
                 else:
                     # Fallback to original query (may fail if segments are already deleted)
-                    child_node_ids = (
-                        db.session.query(ChildChunk.index_node_id)
+                    rows = db.session.execute(
+                        select(ChildChunk.index_node_id)
                         .join(DocumentSegment, ChildChunk.segment_id == DocumentSegment.id)
                         .where(
                             DocumentSegment.dataset_id == dataset.id,
                             DocumentSegment.index_node_id.in_(node_ids),
                             ChildChunk.dataset_id == dataset.id,
                         )
-                        .all()
-                    )
-                    child_node_ids = [child_node_id[0] for child_node_id in child_node_ids if child_node_id[0]]
+                    ).all()
+                    child_node_ids = [row[0] for row in rows if row[0]]
 
                 # Delete from vector index
                 if child_node_ids:
@@ -195,18 +196,22 @@ class ParentChildIndexProcessor(BaseIndexProcessor):
 
                 # Delete from database
                 if delete_child_chunks and child_node_ids:
-                    db.session.query(ChildChunk).where(
-                        ChildChunk.dataset_id == dataset.id, ChildChunk.index_node_id.in_(child_node_ids)
-                    ).delete(synchronize_session=False)
+                    db.session.execute(
+                        delete(ChildChunk).where(
+                            ChildChunk.dataset_id == dataset.id, ChildChunk.index_node_id.in_(child_node_ids)
+                        )
+                    )
                     db.session.commit()
             else:
                 vector.delete()
 
                 if delete_child_chunks:
                     # Use existing compound index: (tenant_id, dataset_id, ...)
-                    db.session.query(ChildChunk).where(
-                        ChildChunk.tenant_id == dataset.tenant_id, ChildChunk.dataset_id == dataset.id
-                    ).delete(synchronize_session=False)
+                    db.session.execute(
+                        delete(ChildChunk).where(
+                            ChildChunk.tenant_id == dataset.tenant_id, ChildChunk.dataset_id == dataset.id
+                        )
+                    )
                     db.session.commit()
 
     def retrieve(
diff --git a/api/core/rag/rerank/rerank_model.py b/api/core/rag/rerank/rerank_model.py
index 211a9f5c5c..8283be19f9 100644
--- a/api/core/rag/rerank/rerank_model.py
+++ b/api/core/rag/rerank/rerank_model.py
@@ -134,9 +134,7 @@ class RerankModelRunner(BaseRerankRunner):
             ):
                 if document.metadata.get("doc_type") == DocType.IMAGE:
                     # Query file info within db.session context to ensure thread-safe access
-                    upload_file = (
-                        db.session.query(UploadFile).where(UploadFile.id == document.metadata["doc_id"]).first()
-                    )
+                    upload_file = db.session.get(UploadFile, document.metadata["doc_id"])
                     if upload_file:
                         blob = storage.load_once(upload_file.key)
                         document_file_base64 = base64.b64encode(blob).decode()
@@ -169,7 +167,7 @@ class RerankModelRunner(BaseRerankRunner):
             return rerank_result, unique_documents
         elif query_type == QueryType.IMAGE_QUERY:
             # Query file info within db.session context to ensure thread-safe access
-            upload_file = db.session.query(UploadFile).where(UploadFile.id == query).first()
+            upload_file = db.session.get(UploadFile, query)
             if upload_file:
                 blob = storage.load_once(upload_file.key)
                 file_query = base64.b64encode(blob).decode()
diff --git a/api/core/rag/retrieval/dataset_retrieval.py b/api/core/rag/retrieval/dataset_retrieval.py
index 1abea6639e..593e1f1420 100644
--- a/api/core/rag/retrieval/dataset_retrieval.py
+++ b/api/core/rag/retrieval/dataset_retrieval.py
@@ -1340,7 +1340,7 @@ class DatasetRetrieval:
         metadata_filtering_conditions: MetadataFilteringCondition | None,
         inputs: dict,
     ) -> tuple[dict[str, list[str]] | None, MetadataCondition | None]:
-        document_query = db.session.query(DatasetDocument).where(
+        document_query = select(DatasetDocument).where(
             DatasetDocument.dataset_id.in_(dataset_ids),
             DatasetDocument.indexing_status == "completed",
             DatasetDocument.enabled == True,
@@ -1411,7 +1411,7 @@ class DatasetRetrieval:
                 document_query = document_query.where(and_(*filters))
             else:
                 document_query = document_query.where(or_(*filters))
-        documents = document_query.all()
+        documents = db.session.scalars(document_query).all()
         # group by dataset_id
         metadata_filter_document_ids = defaultdict(list) if documents else None  # type: ignore
         for document in documents:
diff --git a/api/tests/unit_tests/core/rag/datasource/keyword/jieba/test_jieba.py b/api/tests/unit_tests/core/rag/datasource/keyword/jieba/test_jieba.py
index 795a325a6b..bbdd476914 100644
--- a/api/tests/unit_tests/core/rag/datasource/keyword/jieba/test_jieba.py
+++ b/api/tests/unit_tests/core/rag/datasource/keyword/jieba/test_jieba.py
@@ -201,27 +201,23 @@ def test_search_returns_documents_in_rank_order_and_applies_filter(monkeypatch,
         document_id = _Field("document_id")
 
     keyword = Jieba(_dataset(_dataset_keyword_table()))
-    query_stmt = _FakeQuery()
-    patched_runtime.session.query.return_value = query_stmt
-    patched_runtime.session.execute.return_value = _FakeExecuteResult(
-        [
-            SimpleNamespace(
-                index_node_id="node-2",
-                content="segment-content",
-                index_node_hash="hash-2",
-                document_id="doc-2",
-                dataset_id="dataset-1",
-            )
-        ]
-    )
+    patched_runtime.session.scalars.return_value.all.return_value = [
+        SimpleNamespace(
+            index_node_id="node-2",
+            content="segment-content",
+            index_node_hash="hash-2",
+            document_id="doc-2",
+            dataset_id="dataset-1",
+        )
+    ]
 
     monkeypatch.setattr(jieba_module, "DocumentSegment", _FakeDocumentSegment)
+    monkeypatch.setattr(jieba_module, "select", lambda *_: _FakeSelect())
     monkeypatch.setattr(keyword, "_get_dataset_keyword_table", MagicMock(return_value={"k": {"node-1", "node-2"}}))
     monkeypatch.setattr(keyword, "_retrieve_ids_by_query", MagicMock(return_value=["node-1", "node-2"]))
 
     documents = keyword.search("query", top_k=2, document_ids_filter=["doc-2"])
 
-    assert len(query_stmt.where_calls) == 2
     assert len(documents) == 1
     assert documents[0].page_content == "segment-content"
     assert documents[0].metadata["doc_id"] == "node-2"
diff --git a/api/tests/unit_tests/core/rag/datasource/test_datasource_retrieval.py b/api/tests/unit_tests/core/rag/datasource/test_datasource_retrieval.py
index 63de4b8af2..5dbd62580a 100644
--- a/api/tests/unit_tests/core/rag/datasource/test_datasource_retrieval.py
+++ b/api/tests/unit_tests/core/rag/datasource/test_datasource_retrieval.py
@@ -714,13 +714,13 @@ class TestRetrievalServiceInternals:
             dataset_id="dataset-id",
         )
 
-        dataset_query = Mock()
-        dataset_query.where.return_value.options.return_value.all.return_value = [
+        scalars_result = Mock()
+        scalars_result.all.return_value = [
             dataset_doc_parent,
             dataset_doc_text,
             dataset_doc_parent_summary,
         ]
-        monkeypatch.setattr(retrieval_service_module.db.session, "query", Mock(return_value=dataset_query))
+        monkeypatch.setattr(retrieval_service_module.db.session, "scalars", Mock(return_value=scalars_result))
         monkeypatch.setattr(retrieval_service_module, "RetrievalChildChunk", _SimpleRetrievalChildChunk)
         monkeypatch.setattr(retrieval_service_module, "RetrievalSegments", _SimpleRetrievalSegment)
 
@@ -882,7 +882,7 @@ class TestRetrievalServiceInternals:
     def test_format_retrieval_documents_rolls_back_and_raises_when_db_fails(self, monkeypatch):
         rollback = Mock()
         monkeypatch.setattr(retrieval_service_module.db.session, "rollback", rollback)
-        monkeypatch.setattr(retrieval_service_module.db.session, "query", Mock(side_effect=RuntimeError("db error")))
+        monkeypatch.setattr(retrieval_service_module.db.session, "scalars", Mock(side_effect=RuntimeError("db error")))
 
         documents = [Document(page_content="content", metadata={"document_id": "doc-1"}, provider="dify")]
 
diff --git a/api/tests/unit_tests/core/rag/datasource/vdb/test_vector_factory.py b/api/tests/unit_tests/core/rag/datasource/vdb/test_vector_factory.py
index 54ad6d330b..4e9ceddda9 100644
--- a/api/tests/unit_tests/core/rag/datasource/vdb/test_vector_factory.py
+++ b/api/tests/unit_tests/core/rag/datasource/vdb/test_vector_factory.py
@@ -340,15 +340,13 @@ def test_search_by_file_handles_missing_and_existing_upload(vector_factory_modul
     vector._embeddings = MagicMock()
     vector._vector_processor = MagicMock()
 
+    mock_session = SimpleNamespace(get=lambda _model, _id: None)
     monkeypatch.setattr(vector_factory_module, "UploadFile", SimpleNamespace(id=_Field()))
-    monkeypatch.setattr(
-        vector_factory_module, "db", SimpleNamespace(session=SimpleNamespace(query=lambda _model: upload_query))
-    )
+    monkeypatch.setattr(vector_factory_module, "db", SimpleNamespace(session=mock_session))
 
-    upload_query.first.return_value = None
     assert vector.search_by_file("file-1") == []
 
-    upload_query.first.return_value = SimpleNamespace(key="blob-key")
+    mock_session.get = lambda _model, _id: SimpleNamespace(key="blob-key")
     monkeypatch.setattr(vector_factory_module.storage, "load_once", MagicMock(return_value=b"file-bytes"))
     vector._embeddings.embed_multimodal_query.return_value = [0.3, 0.4]
     vector._vector_processor.search_by_vector.return_value = ["hit"]
diff --git a/api/tests/unit_tests/core/rag/docstore/test_dataset_docstore.py b/api/tests/unit_tests/core/rag/docstore/test_dataset_docstore.py
index 3ba0628fe2..a7b7c1595b 100644
--- a/api/tests/unit_tests/core/rag/docstore/test_dataset_docstore.py
+++ b/api/tests/unit_tests/core/rag/docstore/test_dataset_docstore.py
@@ -167,7 +167,7 @@ class TestDatasetDocumentStoreAddDocuments:
         ):
             mock_session = MagicMock()
             mock_db.session = mock_session
-            mock_db.session.query.return_value.where.return_value.scalar.return_value = None
+            mock_db.session.scalar.return_value = None
 
             mock_manager = MagicMock()
             mock_manager.get_model_instance.return_value = mock_model_instance
@@ -211,7 +211,7 @@ class TestDatasetDocumentStoreAddDocuments:
         with patch("core.rag.docstore.dataset_docstore.db") as mock_db:
             mock_session = MagicMock()
             mock_db.session = mock_session
-            mock_db.session.query.return_value.where.return_value.scalar.return_value = 5
+            mock_db.session.scalar.return_value = 5
 
             with patch.object(DatasetDocumentStore, "get_document_segment", return_value=mock_existing_segment):
                 with patch.object(DatasetDocumentStore, "add_multimodel_documents_binding"):
@@ -276,7 +276,7 @@ class TestDatasetDocumentStoreAddDocuments:
         with patch("core.rag.docstore.dataset_docstore.db") as mock_db:
             mock_session = MagicMock()
             mock_db.session = mock_session
-            mock_db.session.query.return_value.where.return_value.scalar.return_value = None
+            mock_db.session.scalar.return_value = None
 
             with patch.object(DatasetDocumentStore, "get_document_segment", return_value=None):
                 with patch.object(DatasetDocumentStore, "add_multimodel_documents_binding"):
@@ -353,7 +353,7 @@ class TestDatasetDocumentStoreAddDocuments:
         with patch("core.rag.docstore.dataset_docstore.db") as mock_db:
             mock_session = MagicMock()
             mock_db.session = mock_session
-            mock_db.session.query.return_value.where.return_value.scalar.return_value = None
+            mock_db.session.scalar.return_value = None
 
             with patch.object(DatasetDocumentStore, "get_document_segment", return_value=None):
                 with patch.object(DatasetDocumentStore, "add_multimodel_documents_binding"):
@@ -755,7 +755,7 @@ class TestDatasetDocumentStoreAddDocumentsUpdateChild:
         with patch("core.rag.docstore.dataset_docstore.db") as mock_db:
             mock_session = MagicMock()
             mock_db.session = mock_session
-            mock_db.session.query.return_value.where.return_value.scalar.return_value = 5
+            mock_db.session.scalar.return_value = 5
 
             with patch.object(DatasetDocumentStore, "get_document_segment", return_value=mock_existing_segment):
                 with patch.object(DatasetDocumentStore, "add_multimodel_documents_binding"):
@@ -767,7 +767,7 @@ class TestDatasetDocumentStoreAddDocumentsUpdateChild:
 
                     store.add_documents([mock_doc], save_child=True)
 
-                    mock_db.session.query.return_value.where.return_value.delete.assert_called()
+                    mock_db.session.execute.assert_called()
                     mock_db.session.commit.assert_called()
 
 
@@ -798,7 +798,7 @@ class TestDatasetDocumentStoreAddDocumentsUpdateAnswer:
         with patch("core.rag.docstore.dataset_docstore.db") as mock_db:
             mock_session = MagicMock()
             mock_db.session = mock_session
-            mock_db.session.query.return_value.where.return_value.scalar.return_value = 5
+            mock_db.session.scalar.return_value = 5
 
             with patch.object(DatasetDocumentStore, "get_document_segment", return_value=mock_existing_segment):
                 with patch.object(DatasetDocumentStore, "add_multimodel_documents_binding"):
diff --git a/api/tests/unit_tests/core/rag/embedding/test_cached_embedding.py b/api/tests/unit_tests/core/rag/embedding/test_cached_embedding.py
index 6fd44be4d4..3563186186 100644
--- a/api/tests/unit_tests/core/rag/embedding/test_cached_embedding.py
+++ b/api/tests/unit_tests/core/rag/embedding/test_cached_embedding.py
@@ -69,7 +69,7 @@ class TestCacheEmbeddingMultimodalDocuments:
         documents = [{"file_id": "file123", "content": "test content"}]
 
         with patch("core.rag.embedding.cached_embedding.db.session") as mock_session:
-            mock_session.query.return_value.filter_by.return_value.first.return_value = None
+            mock_session.scalar.return_value = None
             mock_model_instance.invoke_multimodal_embedding.return_value = sample_multimodal_result
 
             result = cache_embedding.embed_multimodal_documents(documents)
@@ -114,7 +114,7 @@ class TestCacheEmbeddingMultimodalDocuments:
         )
 
         with patch("core.rag.embedding.cached_embedding.db.session") as mock_session:
-            mock_session.query.return_value.filter_by.return_value.first.return_value = None
+            mock_session.scalar.return_value = None
             mock_model_instance.invoke_multimodal_embedding.return_value = embedding_result
 
             result = cache_embedding.embed_multimodal_documents(documents)
@@ -134,7 +134,7 @@ class TestCacheEmbeddingMultimodalDocuments:
         mock_cached_embedding.get_embedding.return_value = normalized_cached
 
         with patch("core.rag.embedding.cached_embedding.db.session") as mock_session:
-            mock_session.query.return_value.filter_by.return_value.first.return_value = mock_cached_embedding
+            mock_session.scalar.return_value = mock_cached_embedding
 
             result = cache_embedding.embed_multimodal_documents(documents)
 
@@ -180,18 +180,7 @@ class TestCacheEmbeddingMultimodalDocuments:
         )
 
         with patch("core.rag.embedding.cached_embedding.db.session") as mock_session:
-            call_count = [0]
-
-            def mock_filter_by(**kwargs):
-                call_count[0] += 1
-                mock_query = Mock()
-                if call_count[0] == 1:
-                    mock_query.first.return_value = mock_cached_embedding
-                else:
-                    mock_query.first.return_value = None
-                return mock_query
-
-            mock_session.query.return_value.filter_by = mock_filter_by
+            mock_session.scalar.side_effect = [mock_cached_embedding, None, None]
             mock_model_instance.invoke_multimodal_embedding.return_value = embedding_result
 
             result = cache_embedding.embed_multimodal_documents(documents)
@@ -224,7 +213,7 @@ class TestCacheEmbeddingMultimodalDocuments:
         )
 
         with patch("core.rag.embedding.cached_embedding.db.session") as mock_session:
-            mock_session.query.return_value.filter_by.return_value.first.return_value = None
+            mock_session.scalar.return_value = None
             mock_model_instance.invoke_multimodal_embedding.return_value = embedding_result
 
             with patch("core.rag.embedding.cached_embedding.logger") as mock_logger:
@@ -265,7 +254,7 @@ class TestCacheEmbeddingMultimodalDocuments:
             )
 
         with patch("core.rag.embedding.cached_embedding.db.session") as mock_session:
-            mock_session.query.return_value.filter_by.return_value.first.return_value = None
+            mock_session.scalar.return_value = None
 
             batch_results = [create_batch_result(10), create_batch_result(10), create_batch_result(5)]
             mock_model_instance.invoke_multimodal_embedding.side_effect = batch_results
@@ -281,7 +270,7 @@ class TestCacheEmbeddingMultimodalDocuments:
         documents = [{"file_id": "file123"}]
 
         with patch("core.rag.embedding.cached_embedding.db.session") as mock_session:
-            mock_session.query.return_value.filter_by.return_value.first.return_value = None
+            mock_session.scalar.return_value = None
             mock_model_instance.invoke_multimodal_embedding.side_effect = Exception("API Error")
 
             with pytest.raises(Exception) as exc_info:
@@ -298,7 +287,7 @@ class TestCacheEmbeddingMultimodalDocuments:
         documents = [{"file_id": "file123"}]
 
         with patch("core.rag.embedding.cached_embedding.db.session") as mock_session:
-            mock_session.query.return_value.filter_by.return_value.first.return_value = None
+            mock_session.scalar.return_value = None
             mock_model_instance.invoke_multimodal_embedding.return_value = sample_multimodal_result
 
             mock_session.commit.side_effect = IntegrityError("Duplicate key", None, None)
diff --git a/api/tests/unit_tests/core/rag/embedding/test_embedding_service.py b/api/tests/unit_tests/core/rag/embedding/test_embedding_service.py
index d7ba944e58..408cf14a51 100644
--- a/api/tests/unit_tests/core/rag/embedding/test_embedding_service.py
+++ b/api/tests/unit_tests/core/rag/embedding/test_embedding_service.py
@@ -139,7 +139,7 @@ class TestCacheEmbeddingDocuments:
 
         # Mock database query to return no cached embedding (cache miss)
         with patch("core.rag.embedding.cached_embedding.db.session") as mock_session:
-            mock_session.query.return_value.filter_by.return_value.first.return_value = None
+            mock_session.scalar.return_value = None
 
             # Mock model invocation
             mock_model_instance.invoke_text_embedding.return_value = sample_embedding_result
@@ -203,7 +203,7 @@ class TestCacheEmbeddingDocuments:
         )
 
         with patch("core.rag.embedding.cached_embedding.db.session") as mock_session:
-            mock_session.query.return_value.filter_by.return_value.first.return_value = None
+            mock_session.scalar.return_value = None
             mock_model_instance.invoke_text_embedding.return_value = embedding_result
 
             # Act
@@ -240,7 +240,7 @@ class TestCacheEmbeddingDocuments:
 
         with patch("core.rag.embedding.cached_embedding.db.session") as mock_session:
             # Mock database to return cached embedding (cache hit)
-            mock_session.query.return_value.filter_by.return_value.first.return_value = mock_cached_embedding
+            mock_session.scalar.return_value = mock_cached_embedding
 
             # Act
             result = cache_embedding.embed_documents(texts)
@@ -313,19 +313,7 @@ class TestCacheEmbeddingDocuments:
                 mock_hash.side_effect = generate_hash
 
                 # Mock database to return cached embedding only for first text (hash_1)
-                call_count = [0]
-
-                def mock_filter_by(**kwargs):
-                    call_count[0] += 1
-                    mock_query = Mock()
-                    # First call (hash_1) returns cached, others return None
-                    if call_count[0] == 1:
-                        mock_query.first.return_value = mock_cached_embedding
-                    else:
-                        mock_query.first.return_value = None
-                    return mock_query
-
-                mock_session.query.return_value.filter_by = mock_filter_by
+                mock_session.scalar.side_effect = [mock_cached_embedding, None, None]
                 mock_model_instance.invoke_text_embedding.return_value = embedding_result
 
                 # Act
@@ -392,7 +380,7 @@ class TestCacheEmbeddingDocuments:
             )
 
         with patch("core.rag.embedding.cached_embedding.db.session") as mock_session:
-            mock_session.query.return_value.filter_by.return_value.first.return_value = None
+            mock_session.scalar.return_value = None
 
             # Mock model to return appropriate batch results
             batch_results = [
@@ -455,7 +443,7 @@ class TestCacheEmbeddingDocuments:
         )
 
         with patch("core.rag.embedding.cached_embedding.db.session") as mock_session:
-            mock_session.query.return_value.filter_by.return_value.first.return_value = None
+            mock_session.scalar.return_value = None
             mock_model_instance.invoke_text_embedding.return_value = embedding_result
 
             with patch("core.rag.embedding.cached_embedding.logger") as mock_logger:
@@ -489,7 +477,7 @@ class TestCacheEmbeddingDocuments:
         texts = ["Test text"]
 
         with patch("core.rag.embedding.cached_embedding.db.session") as mock_session:
-            mock_session.query.return_value.filter_by.return_value.first.return_value = None
+            mock_session.scalar.return_value = None
 
             # Mock model to raise connection error
             mock_model_instance.invoke_text_embedding.side_effect = InvokeConnectionError("Failed to connect to API")
@@ -515,7 +503,7 @@ class TestCacheEmbeddingDocuments:
         texts = ["Test text"]
 
         with patch("core.rag.embedding.cached_embedding.db.session") as mock_session:
-            mock_session.query.return_value.filter_by.return_value.first.return_value = None
+            mock_session.scalar.return_value = None
 
             # Mock model to raise rate limit error
             mock_model_instance.invoke_text_embedding.side_effect = InvokeRateLimitError("Rate limit exceeded")
@@ -539,7 +527,7 @@ class TestCacheEmbeddingDocuments:
         texts = ["Test text"]
 
         with patch("core.rag.embedding.cached_embedding.db.session") as mock_session:
-            mock_session.query.return_value.filter_by.return_value.first.return_value = None
+            mock_session.scalar.return_value = None
 
             # Mock model to raise authorization error
             mock_model_instance.invoke_text_embedding.side_effect = InvokeAuthorizationError("Invalid API key")
@@ -564,7 +552,7 @@ class TestCacheEmbeddingDocuments:
         texts = ["Test text"]
 
         with patch("core.rag.embedding.cached_embedding.db.session") as mock_session:
-            mock_session.query.return_value.filter_by.return_value.first.return_value = None
+            mock_session.scalar.return_value = None
             mock_model_instance.invoke_text_embedding.return_value = sample_embedding_result
 
             # Mock database commit to raise IntegrityError
@@ -884,7 +872,7 @@ class TestEmbeddingModelSwitching:
         )
 
         with patch("core.rag.embedding.cached_embedding.db.session") as mock_session:
-            mock_session.query.return_value.filter_by.return_value.first.return_value = None
+            mock_session.scalar.return_value = None
 
             model_instance_ada.invoke_text_embedding.return_value = result_ada
             model_instance_3_small.invoke_text_embedding.return_value = result_3_small
@@ -1047,7 +1035,7 @@ class TestEmbeddingDimensionValidation:
         )
 
         with patch("core.rag.embedding.cached_embedding.db.session") as mock_session:
-            mock_session.query.return_value.filter_by.return_value.first.return_value = None
+            mock_session.scalar.return_value = None
             mock_model_instance.invoke_text_embedding.return_value = embedding_result
 
             # Act
@@ -1100,7 +1088,7 @@ class TestEmbeddingDimensionValidation:
         )
 
         with patch("core.rag.embedding.cached_embedding.db.session") as mock_session:
-            mock_session.query.return_value.filter_by.return_value.first.return_value = None
+            mock_session.scalar.return_value = None
             mock_model_instance.invoke_text_embedding.return_value = embedding_result
 
             # Act
@@ -1186,7 +1174,7 @@ class TestEmbeddingDimensionValidation:
         )
 
         with patch("core.rag.embedding.cached_embedding.db.session") as mock_session:
-            mock_session.query.return_value.filter_by.return_value.first.return_value = None
+            mock_session.scalar.return_value = None
 
             model_instance_ada.invoke_text_embedding.return_value = result_ada
             model_instance_cohere.invoke_text_embedding.return_value = result_cohere
@@ -1284,7 +1272,7 @@ class TestEmbeddingEdgeCases:
         )
 
         with patch("core.rag.embedding.cached_embedding.db.session") as mock_session:
-            mock_session.query.return_value.filter_by.return_value.first.return_value = None
+            mock_session.scalar.return_value = None
             mock_model_instance.invoke_text_embedding.return_value = embedding_result
 
             # Act
@@ -1327,7 +1315,7 @@ class TestEmbeddingEdgeCases:
         )
 
         with patch("core.rag.embedding.cached_embedding.db.session") as mock_session:
-            mock_session.query.return_value.filter_by.return_value.first.return_value = None
+            mock_session.scalar.return_value = None
             mock_model_instance.invoke_text_embedding.return_value = embedding_result
 
             # Act
@@ -1375,7 +1363,7 @@ class TestEmbeddingEdgeCases:
         )
 
         with patch("core.rag.embedding.cached_embedding.db.session") as mock_session:
-            mock_session.query.return_value.filter_by.return_value.first.return_value = None
+            mock_session.scalar.return_value = None
             mock_model_instance.invoke_text_embedding.return_value = embedding_result
 
             # Act
@@ -1427,7 +1415,7 @@ class TestEmbeddingEdgeCases:
         )
 
         with patch("core.rag.embedding.cached_embedding.db.session") as mock_session:
-            mock_session.query.return_value.filter_by.return_value.first.return_value = None
+            mock_session.scalar.return_value = None
             mock_model_instance.invoke_text_embedding.return_value = embedding_result
 
             # Act
@@ -1483,7 +1471,7 @@ class TestEmbeddingEdgeCases:
         )
 
         with patch("core.rag.embedding.cached_embedding.db.session") as mock_session:
-            mock_session.query.return_value.filter_by.return_value.first.return_value = None
+            mock_session.scalar.return_value = None
             mock_model_instance.invoke_text_embedding.return_value = embedding_result
 
             # Act
@@ -1551,7 +1539,7 @@ class TestEmbeddingEdgeCases:
         )
 
         with patch("core.rag.embedding.cached_embedding.db.session") as mock_session:
-            mock_session.query.return_value.filter_by.return_value.first.return_value = None
+            mock_session.scalar.return_value = None
             mock_model_instance.invoke_text_embedding.return_value = embedding_result
 
             # Act
@@ -1649,7 +1637,7 @@ class TestEmbeddingEdgeCases:
         )
 
         with patch("core.rag.embedding.cached_embedding.db.session") as mock_session:
-            mock_session.query.return_value.filter_by.return_value.first.return_value = None
+            mock_session.scalar.return_value = None
             mock_model_instance.invoke_text_embedding.return_value = embedding_result
 
             # Act
@@ -1728,7 +1716,7 @@ class TestEmbeddingCachePerformance:
 
         with patch("core.rag.embedding.cached_embedding.db.session") as mock_session:
             # First call: cache miss
-            mock_session.query.return_value.filter_by.return_value.first.return_value = None
+            mock_session.scalar.return_value = None
 
             usage = EmbeddingUsage(
                 tokens=5,
@@ -1756,7 +1744,7 @@ class TestEmbeddingCachePerformance:
             assert len(result1) == 1
 
             # Arrange - Second call: cache hit
-            mock_session.query.return_value.filter_by.return_value.first.return_value = mock_cached_embedding
+            mock_session.scalar.return_value = mock_cached_embedding
 
             # Act - Second call (cache hit)
             result2 = cache_embedding.embed_documents([text])
@@ -1816,7 +1804,7 @@ class TestEmbeddingCachePerformance:
             )
 
         with patch("core.rag.embedding.cached_embedding.db.session") as mock_session:
-            mock_session.query.return_value.filter_by.return_value.first.return_value = None
+            mock_session.scalar.return_value = None
 
             # Mock model to return appropriate batch results
             batch_results = [
diff --git a/api/tests/unit_tests/core/rag/extractor/test_notion_extractor.py b/api/tests/unit_tests/core/rag/extractor/test_notion_extractor.py
index 6daee11f8f..808e41867e 100644
--- a/api/tests/unit_tests/core/rag/extractor/test_notion_extractor.py
+++ b/api/tests/unit_tests/core/rag/extractor/test_notion_extractor.py
@@ -405,35 +405,36 @@ class TestNotionMetadataAndCredentialMethods:
 
         class FakeDocumentModel:
             data_source_info = "data_source_info"
+            id = "id"
 
-        update_calls = []
+        execute_calls = []
 
-        class FakeQuery:
-            def filter_by(self, **kwargs):
+        class FakeUpdateStmt:
+            def where(self, *args):
                 return self
 
-            def update(self, payload):
-                update_calls.append(payload)
+            def values(self, **kwargs):
+                return self
 
         class FakeSession:
             committed = False
 
-            def query(self, model):
-                assert model is FakeDocumentModel
-                return FakeQuery()
+            def execute(self, stmt):
+                execute_calls.append(stmt)
 
             def commit(self):
                 self.committed = True
 
         fake_db = SimpleNamespace(session=FakeSession())
         monkeypatch.setattr(notion_extractor, "DocumentModel", FakeDocumentModel)
+        monkeypatch.setattr(notion_extractor, "update", lambda model: FakeUpdateStmt())
         monkeypatch.setattr(notion_extractor, "db", fake_db)
         monkeypatch.setattr(extractor, "get_notion_last_edited_time", lambda: "2026-01-01T00:00:00.000Z")
 
         doc_model = SimpleNamespace(id="doc-1", data_source_info_dict={"source": "notion"})
         extractor.update_last_edited_time(doc_model)
 
-        assert update_calls
+        assert execute_calls
         assert fake_db.session.committed is True
 
     def test_get_notion_last_edited_time_uses_page_and_database_urls(self, mocker: MockerFixture):
diff --git a/api/tests/unit_tests/core/rag/indexing/processor/test_paragraph_index_processor.py b/api/tests/unit_tests/core/rag/indexing/processor/test_paragraph_index_processor.py
index cc2873dd3f..d4b987c832 100644
--- a/api/tests/unit_tests/core/rag/indexing/processor/test_paragraph_index_processor.py
+++ b/api/tests/unit_tests/core/rag/indexing/processor/test_paragraph_index_processor.py
@@ -188,10 +188,10 @@ class TestParagraphIndexProcessor:
         mock_keyword_cls.return_value.add_texts.assert_called_once_with(docs)
 
     def test_clean_deletes_summaries_and_vector(self, processor: ParagraphIndexProcessor, dataset: Mock) -> None:
-        segment_query = Mock()
-        segment_query.filter.return_value.all.return_value = [SimpleNamespace(id="seg-1")]
+        scalars_result = Mock()
+        scalars_result.all.return_value = [SimpleNamespace(id="seg-1")]
         session = Mock()
-        session.query.return_value = segment_query
+        session.scalars.return_value = scalars_result
 
         with (
             patch("core.rag.index_processor.processor.paragraph_index_processor.db.session", session),
@@ -531,10 +531,10 @@ class TestParagraphIndexProcessor:
             size=1,
             key="key",
         )
-        query = Mock()
-        query.where.return_value.all.return_value = [image_upload, non_image_upload]
+        scalars_result = Mock()
+        scalars_result.all.return_value = [image_upload, non_image_upload]
         session = Mock()
-        session.query.return_value = query
+        session.scalars.return_value = scalars_result
 
         with (
             patch("core.rag.index_processor.processor.paragraph_index_processor.db.session", session),
@@ -565,10 +565,10 @@ class TestParagraphIndexProcessor:
             size=1,
             key="key",
         )
-        query = Mock()
-        query.where.return_value.all.return_value = [image_upload]
+        scalars_result = Mock()
+        scalars_result.all.return_value = [image_upload]
         session = Mock()
-        session.query.return_value = query
+        session.scalars.return_value = scalars_result
 
         with (
             patch("core.rag.index_processor.processor.paragraph_index_processor.db.session", session),
diff --git a/api/tests/unit_tests/core/rag/indexing/processor/test_parent_child_index_processor.py b/api/tests/unit_tests/core/rag/indexing/processor/test_parent_child_index_processor.py
index b1ed735ee7..d363a0804d 100644
--- a/api/tests/unit_tests/core/rag/indexing/processor/test_parent_child_index_processor.py
+++ b/api/tests/unit_tests/core/rag/indexing/processor/test_parent_child_index_processor.py
@@ -208,11 +208,7 @@ class TestParentChildIndexProcessor:
         vector.create_multimodal.assert_called_once_with(multimodal_docs)
 
     def test_clean_with_precomputed_child_ids(self, processor: ParentChildIndexProcessor, dataset: Mock) -> None:
-        delete_query = Mock()
-        where_query = Mock()
-        where_query.delete.return_value = 2
         session = Mock()
-        session.query.return_value.where.return_value = where_query
 
         with (
             patch("core.rag.index_processor.processor.parent_child_index_processor.Vector") as mock_vector_cls,
@@ -227,16 +223,16 @@ class TestParentChildIndexProcessor:
             )
 
         vector.delete_by_ids.assert_called_once_with(["child-1", "child-2"])
-        where_query.delete.assert_called_once_with(synchronize_session=False)
+        session.execute.assert_called()
         session.commit.assert_called_once()
 
     def test_clean_queries_child_ids_when_not_precomputed(
         self, processor: ParentChildIndexProcessor, dataset: Mock
     ) -> None:
-        child_query = Mock()
-        child_query.join.return_value.where.return_value.all.return_value = [("child-1",), (None,), ("child-2",)]
+        execute_result = Mock()
+        execute_result.all.return_value = [("child-1",), (None,), ("child-2",)]
         session = Mock()
-        session.query.return_value = child_query
+        session.execute.return_value = execute_result
 
         with (
             patch("core.rag.index_processor.processor.parent_child_index_processor.Vector") as mock_vector_cls,
@@ -248,10 +244,7 @@ class TestParentChildIndexProcessor:
         vector.delete_by_ids.assert_called_once_with(["child-1", "child-2"])
 
     def test_clean_dataset_wide_cleanup(self, processor: ParentChildIndexProcessor, dataset: Mock) -> None:
-        where_query = Mock()
-        where_query.delete.return_value = 3
         session = Mock()
-        session.query.return_value.where.return_value = where_query
 
         with (
             patch("core.rag.index_processor.processor.parent_child_index_processor.Vector") as mock_vector_cls,
@@ -261,7 +254,7 @@ class TestParentChildIndexProcessor:
             processor.clean(dataset, None, delete_child_chunks=True)
 
         vector.delete.assert_called_once()
-        where_query.delete.assert_called_once_with(synchronize_session=False)
+        session.execute.assert_called()
         session.commit.assert_called_once()
 
     def test_clean_deletes_summaries_when_requested(self, processor: ParentChildIndexProcessor, dataset: Mock) -> None:
diff --git a/api/tests/unit_tests/core/rag/indexing/test_index_processor_base.py b/api/tests/unit_tests/core/rag/indexing/test_index_processor_base.py
index b31bb6eea7..12c5238f5e 100644
--- a/api/tests/unit_tests/core/rag/indexing/test_index_processor_base.py
+++ b/api/tests/unit_tests/core/rag/indexing/test_index_processor_base.py
@@ -133,10 +133,10 @@ class TestBaseIndexProcessor:
         upload_b = SimpleNamespace(id="bbbbbbbb-bbbb-bbbb-bbbb-bbbbbbbbbbbb", name="b.png")
         upload_tool = SimpleNamespace(id="tool-upload-id", name="tool.png")
         upload_remote = SimpleNamespace(id="remote-upload-id", name="remote.png")
-        db_query = Mock()
-        db_query.where.return_value.all.return_value = [upload_a, upload_b, upload_tool, upload_remote]
+        scalars_result = Mock()
+        scalars_result.all.return_value = [upload_a, upload_b, upload_tool, upload_remote]
         db_session = Mock()
-        db_session.query.return_value = db_query
+        db_session.scalars.return_value = scalars_result
 
         with (
             patch.object(processor, "_extract_markdown_images", return_value=images),
@@ -170,10 +170,10 @@ class TestBaseIndexProcessor:
     def test_get_content_files_ignores_missing_upload_records(self, processor: _ForwardingBaseIndexProcessor) -> None:
         document = Document(page_content="ignored", metadata={"document_id": "doc-1", "dataset_id": "ds-1"})
         images = ["/files/aaaaaaaa-aaaa-aaaa-aaaa-aaaaaaaaaaaa/image-preview"]
-        db_query = Mock()
-        db_query.where.return_value.all.return_value = []
+        scalars_result = Mock()
+        scalars_result.all.return_value = []
         db_session = Mock()
-        db_session.query.return_value = db_query
+        db_session.scalars.return_value = scalars_result
 
         with (
             patch.object(processor, "_extract_markdown_images", return_value=images),
@@ -259,20 +259,16 @@ class TestBaseIndexProcessor:
             assert processor._download_image("https://example.com/image.png", current_user=Mock()) is None
 
     def test_download_tool_file_returns_none_when_not_found(self, processor: _ForwardingBaseIndexProcessor) -> None:
-        db_query = Mock()
-        db_query.where.return_value.first.return_value = None
         db_session = Mock()
-        db_session.query.return_value = db_query
+        db_session.get.return_value = None
 
         with patch("core.rag.index_processor.index_processor_base.db.session", db_session):
             assert processor._download_tool_file("tool-id", current_user=Mock()) is None
 
     def test_download_tool_file_uploads_file_when_found(self, processor: _ForwardingBaseIndexProcessor) -> None:
         tool_file = SimpleNamespace(file_key="k1", name="tool.png", mimetype="image/png")
-        db_query = Mock()
-        db_query.where.return_value.first.return_value = tool_file
         db_session = Mock()
-        db_session.query.return_value = db_query
+        db_session.get.return_value = tool_file
         mock_db = Mock()
         mock_db.session = db_session
         mock_db.engine = Mock()
diff --git a/api/tests/unit_tests/core/rag/rerank/test_reranker.py b/api/tests/unit_tests/core/rag/rerank/test_reranker.py
index 2ec7f0498e..c279b00d3b 100644
--- a/api/tests/unit_tests/core/rag/rerank/test_reranker.py
+++ b/api/tests/unit_tests/core/rag/rerank/test_reranker.py
@@ -473,12 +473,10 @@ class TestRerankModelRunnerMultimodal:
             metadata={},
             provider="external",
         )
-        query = Mock()
-        query.where.return_value.first.return_value = SimpleNamespace(key="image-key")
         rerank_result = RerankResult(model="rerank-model", docs=[])
 
         with (
-            patch("core.rag.rerank.rerank_model.db.session.query", return_value=query),
+            patch("core.rag.rerank.rerank_model.db.session.get", return_value=SimpleNamespace(key="image-key")),
             patch("core.rag.rerank.rerank_model.storage.load_once", return_value=b"image-bytes") as mock_load_once,
             patch.object(
                 rerank_runner,
@@ -504,12 +502,10 @@ class TestRerankModelRunnerMultimodal:
             metadata={"doc_id": "img-missing", "doc_type": DocType.IMAGE},
             provider="dify",
         )
-        query = Mock()
-        query.where.return_value.first.return_value = None
         rerank_result = RerankResult(model="rerank-model", docs=[])
 
         with (
-            patch("core.rag.rerank.rerank_model.db.session.query", return_value=query),
+            patch("core.rag.rerank.rerank_model.db.session.get", return_value=None),
             patch.object(
                 rerank_runner,
                 "fetch_text_rerank",
@@ -533,8 +529,6 @@ class TestRerankModelRunnerMultimodal:
             metadata={"doc_id": "txt-1", "doc_type": DocType.TEXT},
             provider="dify",
         )
-        query_chain = Mock()
-        query_chain.where.return_value.first.return_value = SimpleNamespace(key="query-image-key")
         rerank_result = RerankResult(
             model="rerank-model",
             docs=[RerankDocument(index=0, text="text-content", score=0.77)],
@@ -542,7 +536,7 @@ class TestRerankModelRunnerMultimodal:
         mock_model_instance.invoke_multimodal_rerank.return_value = rerank_result
 
         session = MagicMock()
-        session.query.return_value = query_chain
+        session.get.return_value = SimpleNamespace(key="query-image-key")
         with (
             patch("core.rag.rerank.rerank_model.db.session", session),
             patch("core.rag.rerank.rerank_model.storage.load_once", return_value=b"query-image-bytes"),
@@ -563,10 +557,7 @@ class TestRerankModelRunnerMultimodal:
         assert "user" not in invoke_kwargs
 
     def test_fetch_multimodal_rerank_raises_when_query_image_not_found(self, rerank_runner):
-        query_chain = Mock()
-        query_chain.where.return_value.first.return_value = None
-
-        with patch("core.rag.rerank.rerank_model.db.session.query", return_value=query_chain):
+        with patch("core.rag.rerank.rerank_model.db.session.get", return_value=None):
             with pytest.raises(ValueError, match="Upload file not found for query"):
                 rerank_runner.fetch_multimodal_rerank(
                     query="missing-upload-id",
diff --git a/api/tests/unit_tests/core/rag/retrieval/test_dataset_retrieval.py b/api/tests/unit_tests/core/rag/retrieval/test_dataset_retrieval.py
index c11426163e..fee7b168ad 100644
--- a/api/tests/unit_tests/core/rag/retrieval/test_dataset_retrieval.py
+++ b/api/tests/unit_tests/core/rag/retrieval/test_dataset_retrieval.py
@@ -3971,11 +3971,10 @@ class TestDatasetRetrievalAdditionalHelpers:
                 )
 
     def test_get_metadata_filter_condition(self, retrieval: DatasetRetrieval) -> None:
-        db_query = Mock()
-        db_query.where.return_value = db_query
-        db_query.all.return_value = [SimpleNamespace(dataset_id="d1", id="doc-1")]
+        scalars_result = Mock()
+        scalars_result.all.return_value = [SimpleNamespace(dataset_id="d1", id="doc-1")]
 
-        with patch("core.rag.retrieval.dataset_retrieval.db.session.query", return_value=db_query):
+        with patch("core.rag.retrieval.dataset_retrieval.db.session.scalars", return_value=scalars_result):
             mapping, condition = retrieval.get_metadata_filter_condition(
                 dataset_ids=["d1"],
                 query="python",
@@ -3991,7 +3990,7 @@ class TestDatasetRetrievalAdditionalHelpers:
 
         automatic_filters = [{"condition": "contains", "metadata_name": "author", "value": "Alice"}]
         with (
-            patch("core.rag.retrieval.dataset_retrieval.db.session.query", return_value=db_query),
+            patch("core.rag.retrieval.dataset_retrieval.db.session.scalars", return_value=scalars_result),
             patch.object(retrieval, "_automatic_metadata_filter_func", return_value=automatic_filters),
         ):
             mapping, condition = retrieval.get_metadata_filter_condition(
@@ -4012,7 +4011,7 @@ class TestDatasetRetrievalAdditionalHelpers:
             logical_operator="and",
             conditions=[AppCondition(name="author", comparison_operator="contains", value="{{name}}")],
         )
-        with patch("core.rag.retrieval.dataset_retrieval.db.session.query", return_value=db_query):
+        with patch("core.rag.retrieval.dataset_retrieval.db.session.scalars", return_value=scalars_result):
             mapping, condition = retrieval.get_metadata_filter_condition(
                 dataset_ids=["d1"],
                 query="python",
@@ -4027,7 +4026,7 @@ class TestDatasetRetrievalAdditionalHelpers:
         assert condition is not None
         assert condition.conditions[0].value == "Alice"
 
-        with patch("core.rag.retrieval.dataset_retrieval.db.session.query", return_value=db_query):
+        with patch("core.rag.retrieval.dataset_retrieval.db.session.scalars", return_value=scalars_result):
             with pytest.raises(ValueError, match="Invalid metadata filtering mode"):
                 retrieval.get_metadata_filter_condition(
                     dataset_ids=["d1"],