diff --git a/api/services/audio_service.py b/api/services/audio_service.py
index 90e72d5f34..1c7027efb4 100644
--- a/api/services/audio_service.py
+++ b/api/services/audio_service.py
@@ -132,7 +132,7 @@ class AudioService:
                 uuid.UUID(message_id)
             except ValueError:
                 return None
-            message = db.session.query(Message).where(Message.id == message_id).first()
+            message = db.session.get(Message, message_id)
             if message is None:
                 return None
             if message.answer == "" and message.status in {MessageStatus.NORMAL, MessageStatus.PAUSED}:
diff --git a/api/services/billing_service.py b/api/services/billing_service.py
index 54c595e0cb..9970b2e604 100644
--- a/api/services/billing_service.py
+++ b/api/services/billing_service.py
@@ -6,6 +6,7 @@ from typing import Literal
 
 import httpx
 from pydantic import TypeAdapter
+from sqlalchemy import select
 from tenacity import retry, retry_if_exception_type, stop_before_delay, wait_fixed
 from typing_extensions import TypedDict
 from werkzeug.exceptions import InternalServerError
@@ -158,10 +159,10 @@ class BillingService:
     def is_tenant_owner_or_admin(current_user: Account):
         tenant_id = current_user.current_tenant_id
 
-        join: TenantAccountJoin | None = (
-            db.session.query(TenantAccountJoin)
+        join: TenantAccountJoin | None = db.session.scalar(
+            select(TenantAccountJoin)
             .where(TenantAccountJoin.tenant_id == tenant_id, TenantAccountJoin.account_id == current_user.id)
-            .first()
+            .limit(1)
         )
 
         if not join:
diff --git a/api/services/conversation_service.py b/api/services/conversation_service.py
index ba1e7bb826..95482a2235 100644
--- a/api/services/conversation_service.py
+++ b/api/services/conversation_service.py
@@ -137,11 +137,11 @@ class ConversationService:
     @classmethod
     def auto_generate_name(cls, app_model: App, conversation: Conversation):
         # get conversation first message
-        message = (
-            db.session.query(Message)
+        message = db.session.scalar(
+            select(Message)
             .where(Message.app_id == app_model.id, Message.conversation_id == conversation.id)
             .order_by(Message.created_at.asc())
-            .first()
+            .limit(1)
         )
 
         if not message:
@@ -160,8 +160,8 @@ class ConversationService:
 
     @classmethod
     def get_conversation(cls, app_model: App, conversation_id: str, user: Union[Account, EndUser] | None):
-        conversation = (
-            db.session.query(Conversation)
+        conversation = db.session.scalar(
+            select(Conversation)
             .where(
                 Conversation.id == conversation_id,
                 Conversation.app_id == app_model.id,
@@ -170,7 +170,7 @@ class ConversationService:
                 Conversation.from_account_id == (user.id if isinstance(user, Account) else None),
                 Conversation.is_deleted == False,
             )
-            .first()
+            .limit(1)
         )
 
         if not conversation:
diff --git a/api/services/credit_pool_service.py b/api/services/credit_pool_service.py
index 2894826935..7826695366 100644
--- a/api/services/credit_pool_service.py
+++ b/api/services/credit_pool_service.py
@@ -1,6 +1,6 @@
 import logging
 
-from sqlalchemy import update
+from sqlalchemy import select, update
 from sqlalchemy.orm import Session
 
 from configs import dify_config
@@ -29,13 +29,13 @@ class CreditPoolService:
     @classmethod
     def get_pool(cls, tenant_id: str, pool_type: str = "trial") -> TenantCreditPool | None:
         """get tenant credit pool"""
-        return (
-            db.session.query(TenantCreditPool)
-            .filter_by(
-                tenant_id=tenant_id,
-                pool_type=pool_type,
+        return db.session.scalar(
+            select(TenantCreditPool)
+            .where(
+                TenantCreditPool.tenant_id == tenant_id,
+                TenantCreditPool.pool_type == pool_type,
             )
-            .first()
+            .limit(1)
         )
 
     @classmethod
diff --git a/api/services/enterprise/account_deletion_sync.py b/api/services/enterprise/account_deletion_sync.py
index c7ff42894d..b5107fb0f6 100644
--- a/api/services/enterprise/account_deletion_sync.py
+++ b/api/services/enterprise/account_deletion_sync.py
@@ -4,6 +4,7 @@ import uuid
 from datetime import UTC, datetime
 
 from redis import RedisError
+from sqlalchemy import select
 
 from configs import dify_config
 from extensions.ext_database import db
@@ -104,7 +105,9 @@ def sync_account_deletion(account_id: str, *, source: str) -> bool:
         return True
 
     # Fetch all workspaces the account belongs to
-    workspace_joins = db.session.query(TenantAccountJoin).filter_by(account_id=account_id).all()
+    workspace_joins = db.session.scalars(
+        select(TenantAccountJoin).where(TenantAccountJoin.account_id == account_id)
+    ).all()
 
     # Queue sync task for each workspace
     success = True
diff --git a/api/services/rag_pipeline/pipeline_generate_service.py b/api/services/rag_pipeline/pipeline_generate_service.py
index 07e1b8f20e..10e89b1dba 100644
--- a/api/services/rag_pipeline/pipeline_generate_service.py
+++ b/api/services/rag_pipeline/pipeline_generate_service.py
@@ -110,7 +110,7 @@ class PipelineGenerateService:
         Update document status to waiting
         :param document_id: document id
         """
-        document = db.session.query(Document).where(Document.id == document_id).first()
+        document = db.session.get(Document, document_id)
         if document:
             document.indexing_status = IndexingStatus.WAITING
             db.session.add(document)
diff --git a/api/services/rag_pipeline/pipeline_template/customized/customized_retrieval.py b/api/services/rag_pipeline/pipeline_template/customized/customized_retrieval.py
index 4ac2e0792b..2ee871a266 100644
--- a/api/services/rag_pipeline/pipeline_template/customized/customized_retrieval.py
+++ b/api/services/rag_pipeline/pipeline_template/customized/customized_retrieval.py
@@ -1,4 +1,5 @@
 import yaml
+from sqlalchemy import select
 
 from extensions.ext_database import db
 from libs.login import current_account_with_tenant
@@ -32,12 +33,11 @@ class CustomizedPipelineTemplateRetrieval(PipelineTemplateRetrievalBase):
         :param language: language
         :return:
         """
-        pipeline_customized_templates = (
-            db.session.query(PipelineCustomizedTemplate)
+        pipeline_customized_templates = db.session.scalars(
+            select(PipelineCustomizedTemplate)
             .where(PipelineCustomizedTemplate.tenant_id == tenant_id, PipelineCustomizedTemplate.language == language)
             .order_by(PipelineCustomizedTemplate.position.asc(), PipelineCustomizedTemplate.created_at.desc())
-            .all()
-        )
+        ).all()
         recommended_pipelines_results = []
         for pipeline_customized_template in pipeline_customized_templates:
             recommended_pipeline_result = {
@@ -59,9 +59,7 @@ class CustomizedPipelineTemplateRetrieval(PipelineTemplateRetrievalBase):
         :param template_id: Template ID
         :return:
         """
-        pipeline_template = (
-            db.session.query(PipelineCustomizedTemplate).where(PipelineCustomizedTemplate.id == template_id).first()
-        )
+        pipeline_template = db.session.get(PipelineCustomizedTemplate, template_id)
         if not pipeline_template:
             return None
 
diff --git a/api/services/rag_pipeline/pipeline_template/database/database_retrieval.py b/api/services/rag_pipeline/pipeline_template/database/database_retrieval.py
index 908f9a2684..43b21a7b32 100644
--- a/api/services/rag_pipeline/pipeline_template/database/database_retrieval.py
+++ b/api/services/rag_pipeline/pipeline_template/database/database_retrieval.py
@@ -1,4 +1,5 @@
 import yaml
+from sqlalchemy import select
 
 from extensions.ext_database import db
 from models.dataset import PipelineBuiltInTemplate
@@ -30,8 +31,10 @@ class DatabasePipelineTemplateRetrieval(PipelineTemplateRetrievalBase):
         :return:
         """
 
-        pipeline_built_in_templates: list[PipelineBuiltInTemplate] = (
-            db.session.query(PipelineBuiltInTemplate).where(PipelineBuiltInTemplate.language == language).all()
+        pipeline_built_in_templates = list(
+            db.session.scalars(
+                select(PipelineBuiltInTemplate).where(PipelineBuiltInTemplate.language == language)
+            ).all()
         )
 
         recommended_pipelines_results = []
@@ -58,9 +61,7 @@ class DatabasePipelineTemplateRetrieval(PipelineTemplateRetrievalBase):
         :return:
         """
         # is in public recommended list
-        pipeline_template = (
-            db.session.query(PipelineBuiltInTemplate).where(PipelineBuiltInTemplate.id == template_id).first()
-        )
+        pipeline_template = db.session.get(PipelineBuiltInTemplate, template_id)
 
         if not pipeline_template:
             return None
diff --git a/api/services/recommend_app/database/database_retrieval.py b/api/services/recommend_app/database/database_retrieval.py
index d0c49325dc..6fb90d356d 100644
--- a/api/services/recommend_app/database/database_retrieval.py
+++ b/api/services/recommend_app/database/database_retrieval.py
@@ -77,17 +77,15 @@ class DatabaseRecommendAppRetrieval(RecommendAppRetrievalBase):
         :return:
         """
         # is in public recommended list
-        recommended_app = (
-            db.session.query(RecommendedApp)
-            .where(RecommendedApp.is_listed == True, RecommendedApp.app_id == app_id)
-            .first()
+        recommended_app = db.session.scalar(
+            select(RecommendedApp).where(RecommendedApp.is_listed == True, RecommendedApp.app_id == app_id).limit(1)
         )
 
         if not recommended_app:
             return None
 
         # get app detail
-        app_model = db.session.query(App).where(App.id == app_id).first()
+        app_model = db.session.get(App, app_id)
         if not app_model or not app_model.is_public:
             return None
 
diff --git a/api/services/web_conversation_service.py b/api/services/web_conversation_service.py
index e028e3e5e3..5ef9e9be61 100644
--- a/api/services/web_conversation_service.py
+++ b/api/services/web_conversation_service.py
@@ -64,15 +64,15 @@ class WebConversationService:
     def pin(cls, app_model: App, conversation_id: str, user: Union[Account, EndUser] | None):
         if not user:
             return
-        pinned_conversation = (
-            db.session.query(PinnedConversation)
+        pinned_conversation = db.session.scalar(
+            select(PinnedConversation)
             .where(
                 PinnedConversation.app_id == app_model.id,
                 PinnedConversation.conversation_id == conversation_id,
                 PinnedConversation.created_by_role == ("account" if isinstance(user, Account) else "end_user"),
                 PinnedConversation.created_by == user.id,
             )
-            .first()
+            .limit(1)
         )
 
         if pinned_conversation:
@@ -96,15 +96,15 @@ class WebConversationService:
     def unpin(cls, app_model: App, conversation_id: str, user: Union[Account, EndUser] | None):
         if not user:
             return
-        pinned_conversation = (
-            db.session.query(PinnedConversation)
+        pinned_conversation = db.session.scalar(
+            select(PinnedConversation)
             .where(
                 PinnedConversation.app_id == app_model.id,
                 PinnedConversation.conversation_id == conversation_id,
                 PinnedConversation.created_by_role == ("account" if isinstance(user, Account) else "end_user"),
                 PinnedConversation.created_by == user.id,
             )
-            .first()
+            .limit(1)
         )
 
         if not pinned_conversation:
diff --git a/api/services/webapp_auth_service.py b/api/services/webapp_auth_service.py
index 5ca0b63001..eaea79af2f 100644
--- a/api/services/webapp_auth_service.py
+++ b/api/services/webapp_auth_service.py
@@ -3,6 +3,7 @@ import secrets
 from datetime import UTC, datetime, timedelta
 from typing import Any
 
+from sqlalchemy import select
 from werkzeug.exceptions import NotFound, Unauthorized
 
 from configs import dify_config
@@ -92,10 +93,10 @@ class WebAppAuthService:
 
     @classmethod
     def create_end_user(cls, app_code, email) -> EndUser:
-        site = db.session.query(Site).where(Site.code == app_code).first()
+        site = db.session.scalar(select(Site).where(Site.code == app_code).limit(1))
         if not site:
             raise NotFound("Site not found.")
-        app_model = db.session.query(App).where(App.id == site.app_id).first()
+        app_model = db.session.get(App, site.app_id)
         if not app_model:
             raise NotFound("App not found.")
         end_user = EndUser(
diff --git a/api/services/workflow/workflow_converter.py b/api/services/workflow/workflow_converter.py
index 31367f72fa..399c82849f 100644
--- a/api/services/workflow/workflow_converter.py
+++ b/api/services/workflow/workflow_converter.py
@@ -6,6 +6,7 @@ from graphon.model_runtime.entities.llm_entities import LLMMode
 from graphon.model_runtime.utils.encoders import jsonable_encoder
 from graphon.nodes import BuiltinNodeTypes
 from graphon.variables.input_entities import VariableEntity
+from sqlalchemy import select
 from typing_extensions import TypedDict
 
 from core.app.app_config.entities import (
@@ -648,10 +649,10 @@ class WorkflowConverter:
         :param api_based_extension_id: api based extension id
         :return:
         """
-        api_based_extension = (
-            db.session.query(APIBasedExtension)
+        api_based_extension = db.session.scalar(
+            select(APIBasedExtension)
             .where(APIBasedExtension.tenant_id == tenant_id, APIBasedExtension.id == api_based_extension_id)
-            .first()
+            .limit(1)
         )
 
         if not api_based_extension:
diff --git a/api/services/workspace_service.py b/api/services/workspace_service.py
index 84a8b03329..eb4671cfaa 100644
--- a/api/services/workspace_service.py
+++ b/api/services/workspace_service.py
@@ -1,4 +1,5 @@
 from flask_login import current_user
+from sqlalchemy import select
 
 from configs import dify_config
 from enums.cloud_plan import CloudPlan
@@ -24,10 +25,10 @@ class WorkspaceService:
         }
 
         # Get role of user
-        tenant_account_join = (
-            db.session.query(TenantAccountJoin)
+        tenant_account_join = db.session.scalar(
+            select(TenantAccountJoin)
             .where(TenantAccountJoin.tenant_id == tenant.id, TenantAccountJoin.account_id == current_user.id)
-            .first()
+            .limit(1)
         )
         assert tenant_account_join is not None, "TenantAccountJoin not found"
         tenant_info["role"] = tenant_account_join.role
diff --git a/api/tests/unit_tests/services/test_audio_service.py b/api/tests/unit_tests/services/test_audio_service.py
index 175fd3ee01..cede6671ce 100644
--- a/api/tests/unit_tests/services/test_audio_service.py
+++ b/api/tests/unit_tests/services/test_audio_service.py
@@ -421,11 +421,8 @@ class TestAudioServiceTTS:
             answer="Message answer text",
         )
 
-        # Mock database query
-        mock_query = MagicMock()
-        mock_db_session.query.return_value = mock_query
-        mock_query.where.return_value = mock_query
-        mock_query.first.return_value = message
+        # Mock database lookup
+        mock_db_session.get.return_value = message
 
         # Mock ModelManager
         mock_model_manager = mock_model_manager_class.return_value
@@ -568,11 +565,8 @@ class TestAudioServiceTTS:
         # Arrange
         app = factory.create_app_mock()
 
-        # Mock database query returning None
-        mock_query = MagicMock()
-        mock_db_session.query.return_value = mock_query
-        mock_query.where.return_value = mock_query
-        mock_query.first.return_value = None
+        # Mock database lookup returning None
+        mock_db_session.get.return_value = None
 
         # Act
         result = AudioService.transcript_tts(
@@ -594,11 +588,8 @@ class TestAudioServiceTTS:
             status=MessageStatus.NORMAL,
         )
 
-        # Mock database query
-        mock_query = MagicMock()
-        mock_db_session.query.return_value = mock_query
-        mock_query.where.return_value = mock_query
-        mock_query.first.return_value = message
+        # Mock database lookup
+        mock_db_session.get.return_value = message
 
         # Act
         result = AudioService.transcript_tts(
diff --git a/api/tests/unit_tests/services/test_billing_service.py b/api/tests/unit_tests/services/test_billing_service.py
index b3d2e60802..168ab6cf0d 100644
--- a/api/tests/unit_tests/services/test_billing_service.py
+++ b/api/tests/unit_tests/services/test_billing_service.py
@@ -865,16 +865,11 @@ class TestBillingServiceAccountManagement:
         mock_join = MagicMock(spec=TenantAccountJoin)
         mock_join.role = TenantAccountRole.OWNER
 
-        mock_query = MagicMock()
-        mock_query.where.return_value.first.return_value = mock_join
-        mock_db_session.query.return_value = mock_query
+        mock_db_session.scalar.return_value = mock_join
 
         # Act - should not raise exception
         BillingService.is_tenant_owner_or_admin(current_user)
 
-        # Assert
-        mock_db_session.query.assert_called_once()
-
     def test_is_tenant_owner_or_admin_admin(self, mock_db_session):
         """Test tenant owner/admin check for admin role."""
         # Arrange
@@ -885,16 +880,11 @@ class TestBillingServiceAccountManagement:
         mock_join = MagicMock(spec=TenantAccountJoin)
         mock_join.role = TenantAccountRole.ADMIN
 
-        mock_query = MagicMock()
-        mock_query.where.return_value.first.return_value = mock_join
-        mock_db_session.query.return_value = mock_query
+        mock_db_session.scalar.return_value = mock_join
 
         # Act - should not raise exception
         BillingService.is_tenant_owner_or_admin(current_user)
 
-        # Assert
-        mock_db_session.query.assert_called_once()
-
     def test_is_tenant_owner_or_admin_normal_user_raises_error(self, mock_db_session):
         """Test tenant owner/admin check raises error for normal user."""
         # Arrange
@@ -905,9 +895,7 @@ class TestBillingServiceAccountManagement:
         mock_join = MagicMock(spec=TenantAccountJoin)
         mock_join.role = TenantAccountRole.NORMAL
 
-        mock_query = MagicMock()
-        mock_query.where.return_value.first.return_value = mock_join
-        mock_db_session.query.return_value = mock_query
+        mock_db_session.scalar.return_value = mock_join
 
         # Act & Assert
         with pytest.raises(ValueError) as exc_info:
@@ -921,9 +909,7 @@ class TestBillingServiceAccountManagement:
         current_user.id = "account-123"
         current_user.current_tenant_id = "tenant-456"
 
-        mock_query = MagicMock()
-        mock_query.where.return_value.first.return_value = None
-        mock_db_session.query.return_value = mock_query
+        mock_db_session.scalar.return_value = None
 
         # Act & Assert
         with pytest.raises(ValueError) as exc_info:
@@ -1135,9 +1121,7 @@ class TestBillingServiceEdgeCases:
         mock_join.role = TenantAccountRole.EDITOR  # Editor is not privileged
 
         with patch("services.billing_service.db.session") as mock_session:
-            mock_query = MagicMock()
-            mock_query.where.return_value.first.return_value = mock_join
-            mock_session.query.return_value = mock_query
+            mock_session.scalar.return_value = mock_join
 
             # Act & Assert
             with pytest.raises(ValueError) as exc_info:
@@ -1155,9 +1139,7 @@ class TestBillingServiceEdgeCases:
         mock_join.role = TenantAccountRole.DATASET_OPERATOR  # Dataset operator is not privileged
 
         with patch("services.billing_service.db.session") as mock_session:
-            mock_query = MagicMock()
-            mock_query.where.return_value.first.return_value = mock_join
-            mock_session.query.return_value = mock_query
+            mock_session.scalar.return_value = mock_join
 
             # Act & Assert
             with pytest.raises(ValueError) as exc_info:
diff --git a/api/tests/unit_tests/services/test_conversation_service.py b/api/tests/unit_tests/services/test_conversation_service.py
index 1bf4c0e172..a4359f00b8 100644
--- a/api/tests/unit_tests/services/test_conversation_service.py
+++ b/api/tests/unit_tests/services/test_conversation_service.py
@@ -355,15 +355,13 @@ class TestConversationServiceGetConversation:
             from_account_id=user.id, from_source=ConversationFromSource.CONSOLE
         )
 
-        mock_query = mock_db_session.query.return_value
-        mock_query.where.return_value.first.return_value = conversation
+        mock_db_session.scalar.return_value = conversation
 
         # Act
         result = ConversationService.get_conversation(app_model, "conv-123", user)
 
         # Assert
         assert result == conversation
-        mock_db_session.query.assert_called_once_with(Conversation)
 
     @patch("services.conversation_service.db.session")
     def test_get_conversation_success_with_end_user(self, mock_db_session):
@@ -379,8 +377,7 @@ class TestConversationServiceGetConversation:
             from_end_user_id=user.id, from_source=ConversationFromSource.API
         )
 
-        mock_query = mock_db_session.query.return_value
-        mock_query.where.return_value.first.return_value = conversation
+        mock_db_session.scalar.return_value = conversation
 
         # Act
         result = ConversationService.get_conversation(app_model, "conv-123", user)
@@ -399,8 +396,7 @@ class TestConversationServiceGetConversation:
         app_model = ConversationServiceTestDataFactory.create_app_mock()
         user = ConversationServiceTestDataFactory.create_account_mock()
 
-        mock_query = mock_db_session.query.return_value
-        mock_query.where.return_value.first.return_value = None
+        mock_db_session.scalar.return_value = None
 
         # Act & Assert
         with pytest.raises(ConversationNotExistsError):
@@ -489,8 +485,7 @@ class TestConversationServiceAutoGenerateName:
         )
 
         # Mock database query to return message
-        mock_query = mock_db_session.query.return_value
-        mock_query.where.return_value.order_by.return_value.first.return_value = message
+        mock_db_session.scalar.return_value = message
 
         # Mock LLM generator
         mock_llm_generator.generate_conversation_name.return_value = "Generated Name"
@@ -518,8 +513,7 @@ class TestConversationServiceAutoGenerateName:
         conversation = ConversationServiceTestDataFactory.create_conversation_mock()
 
         # Mock database query to return None
-        mock_query = mock_db_session.query.return_value
-        mock_query.where.return_value.order_by.return_value.first.return_value = None
+        mock_db_session.scalar.return_value = None
 
         # Act & Assert
         with pytest.raises(MessageNotExistsError):
@@ -541,8 +535,7 @@ class TestConversationServiceAutoGenerateName:
         )
 
         # Mock database query to return message
-        mock_query = mock_db_session.query.return_value
-        mock_query.where.return_value.order_by.return_value.first.return_value = message
+        mock_db_session.scalar.return_value = message
 
         # Mock LLM generator to raise exception
         mock_llm_generator.generate_conversation_name.side_effect = Exception("LLM Error")