diff --git a/api/services/dataset_service.py b/api/services/dataset_service.py
index 880166890e3..a8b83b78047 100644
--- a/api/services/dataset_service.py
+++ b/api/services/dataset_service.py
@@ -739,8 +739,13 @@ class DatasetService:
             dataset.id, external_knowledge_id, external_knowledge_api_id, session
         )
 
-        # Commit changes to database
-        session.commit()
+        # Flush changes to the database without closing the caller-managed
+        # transaction. This helper receives a session opened by the caller
+        # (`with Session(...) as session`); calling commit() here closed that
+        # context manager early and raised
+        # sqlalchemy.exc.InvalidRequestError: Can't operate on closed transaction
+        # (#39191).
+        session.flush()
 
         return dataset
 
@@ -810,9 +815,15 @@ class DatasetService:
         if data.get("icon_info"):
             filtered_data["icon_info"] = data.get("icon_info")
 
-        # Update dataset in database
+        # Update dataset in database. Use flush() rather than commit() so the
+        # caller-managed transaction (opened with `with Session(...) as session`)
+        # stays open for subsequent operations — _update_pipeline_knowledge_base
+        # node data and any caller follow-ups run on the same session. Calling
+        # commit() here closed the context manager early and raised
+        # sqlalchemy.exc.InvalidRequestError: Can't operate on closed transaction
+        # (#39191).
         session.execute(update(Dataset).where(Dataset.id == dataset.id).values(**filtered_data))
-        session.commit()
+        session.flush()
 
         # Reload dataset to get updated values
         session.refresh(dataset)
diff --git a/api/tests/unit_tests/services/test_dataset_service_dataset.py b/api/tests/unit_tests/services/test_dataset_service_dataset.py
index 4ce8d46d702..1fcc81039ca 100644
--- a/api/tests/unit_tests/services/test_dataset_service_dataset.py
+++ b/api/tests/unit_tests/services/test_dataset_service_dataset.py
@@ -631,7 +631,9 @@ class TestDatasetServiceCreationAndUpdate:
         get_external_knowledge_api.assert_called_once_with("api-1", dataset.tenant_id, session=session)
         update_binding.assert_called_once_with("dataset-1", "knowledge-1", "api-1", session)
         session.add.assert_called_once_with(dataset)
-        session.commit.assert_called_once()
+        # flush() (not commit()) preserves the caller-managed transaction (#39191)
+        session.flush.assert_called_once()
+        session.commit.assert_not_called()
 
     @pytest.mark.parametrize(
         ("payload", "message"),
@@ -728,7 +730,9 @@ class TestDatasetServiceCreationAndUpdate:
         assert "external_knowledge_api_id" not in updated_values
         assert "external_knowledge_id" not in updated_values
         assert "external_retrieval_model" not in updated_values
-        session.commit.assert_called_once()
+        # flush() (not commit()) preserves the caller-managed transaction (#39191)
+        session.flush.assert_called_once()
+        session.commit.assert_not_called()
         session.refresh.assert_called_once_with(dataset)
         update_pipeline.assert_called_once_with(dataset, "user-1", session)
         vector_task.delay.assert_called_once_with("dataset-1", "update")