diff --git a/api/services/hit_testing_service.py b/api/services/hit_testing_service.py
index 2f9d5c3677b..71bbf621cae 100644
--- a/api/services/hit_testing_service.py
+++ b/api/services/hit_testing_service.py
@@ -183,7 +183,10 @@ class HitTestingService:
                 created_by=account.id,
             )
             session.add(dataset_query)
-        session.commit()
+            # Stage the query log without committing: the caller owns the session
+            # (e.g. `with_session`), and committing here would close a caller-managed
+            # transaction before the document lookup below runs. See #38998.
+            session.flush()
 
         return cls.compact_retrieve_response(query, all_documents, session=session)
 
diff --git a/api/tests/unit_tests/services/test_hit_testing_service.py b/api/tests/unit_tests/services/test_hit_testing_service.py
index c251ac5147d..68edd7486a9 100644
--- a/api/tests/unit_tests/services/test_hit_testing_service.py
+++ b/api/tests/unit_tests/services/test_hit_testing_service.py
@@ -1,7 +1,14 @@
 """Unit tests for the database-independent hit-testing helpers."""
 
-import pytest
+from unittest.mock import patch
 
+import pytest
+from sqlalchemy import select
+from sqlalchemy.orm import Session
+
+from core.rag.models.document import Document
+from models import Account
+from models.dataset import Dataset, DatasetQuery
 from services.hit_testing_service import HitTestingService
 
 
@@ -30,3 +37,64 @@ class TestHitTestingServiceArguments:
     def test_hit_testing_args_check_should_raise_error_when_attachments_not_list(self) -> None:
         with pytest.raises(ValueError, match="Attachment_ids must be a list"):
             HitTestingService.hit_testing_args_check({"attachment_ids": "not a list"})
+
+
+class _FakeSegment:
+    """Minimal stand-in for a retrieval segment carrying a document id."""
+
+    def __init__(self, document_id: str) -> None:
+        self.document_id = document_id
+
+
+class _FakeRetrievalRecord:
+    """Minimal stand-in for a RetrievalSegments record.
+
+    Implements just the two members ``_dump_retrieval_records`` reads:
+    ``model_dump()`` and ``segment.document_id``.
+    """
+
+    def __init__(self, document_id: str, content: str, score: float) -> None:
+        self.segment = _FakeSegment(document_id)
+        self._content = content
+        self._score = score
+
+    def model_dump(self) -> dict[str, str | float]:
+        return {"content": self._content, "score": self._score}
+
+
+class TestHitTestingServiceRetrieveTransaction:
+    """Regression tests for https://github.com/langgenius/dify/issues/38998."""
+
+    def test_retrieve_should_not_close_caller_managed_transaction(self, sqlite_session: Session) -> None:
+        """retrieve() must not commit the caller-managed session mid-flow.
+
+        When the caller manages the session inside a ``session.begin()`` block, an
+        explicit ``session.commit()`` inside retrieve() closes that transaction and
+        the follow-up document lookup then fails with "Can't operate on closed
+        transaction inside context manager". The query log must be staged with
+        ``flush()`` so the caller commits it.
+        """
+        dataset = Dataset(id="dataset-123", tenant_id="tenant-123", provider="vendor", retrieval_model=None)
+        account = Account(name="Test User", email="test@example.com")
+        account.id = "user-789"
+        query = "test query"
+
+        record = _FakeRetrievalRecord(document_id="doc-1", content="Doc 1", score=0.95)
+
+        with (
+            patch("services.hit_testing_service.RetrievalService.retrieve", autospec=True) as mock_retrieve,
+            patch(
+                "services.hit_testing_service.RetrievalService.format_retrieval_documents", autospec=True
+            ) as mock_format,
+        ):
+            mock_retrieve.return_value = [Document(page_content="Doc 1", metadata={})]
+            mock_format.return_value = [record]
+
+            with sqlite_session.begin():
+                result = HitTestingService.retrieve(dataset, query, account, None, {}, session=sqlite_session)
+
+        assert result["query"]["content"] == query
+        query_log = sqlite_session.scalar(select(DatasetQuery))
+        assert query_log is not None
+        assert query_log.dataset_id == dataset.id
+        assert query_log.created_by == account.id