diff --git a/backend/app/gateway/routers/personal_mcp.py b/backend/app/gateway/routers/personal_mcp.py
index 81585ea2de..f9e6d56b7a 100644
--- a/backend/app/gateway/routers/personal_mcp.py
+++ b/backend/app/gateway/routers/personal_mcp.py
@@ -12,6 +12,7 @@ from app.gateway.routers import mcp
 from deerflow.capabilities.runtime import ambiguous_installation_ids
 from deerflow.config.extensions_config import ExtensionsConfig, atomic_write_extensions_config, extensions_config_file_lock, extensions_config_write_lock
 from deerflow.mcp.user_config import read_user_mcp_config, user_mcp_config_path
+from deerflow.utils.file_io import await_drained
 
 router = APIRouter(prefix="/api/mcp/personal/config", tags=["mcp"])
 
@@ -102,7 +103,7 @@ async def get_configuration(request: Request):
 async def _write(request: Request, operation: str, body):
     owner = await _owner(request)
     admin = await is_admin_user(request)
-    raw = await asyncio.to_thread(_mutate, owner, operation, body, admin=admin)
+    raw = await await_drained(asyncio.to_thread(_mutate, owner, operation, body, admin=admin))
     return _response(raw)
 
 
diff --git a/backend/tests/test_personal_mcp.py b/backend/tests/test_personal_mcp.py
index 9e8c8aa367..e411b5eed4 100644
--- a/backend/tests/test_personal_mcp.py
+++ b/backend/tests/test_personal_mcp.py
@@ -48,6 +48,41 @@ def create(client, user, *, name="github", token=None, role="admin"):
     )
 
 
+@pytest.mark.asyncio
+async def test_personal_config_write_drains_started_mutation_across_cancellation(monkeypatch):
+    started = asyncio.Event()
+
+    monkeypatch.setattr(personal_mcp, "_owner", AsyncMock(return_value="alice"))
+    monkeypatch.setattr(personal_mcp, "is_admin_user", AsyncMock(return_value=True))
+
+    def mutate(*_args, **_kwargs):
+        started_loop.call_soon_threadsafe(started.set)
+        release_thread.wait(timeout=5)
+        return {"mcpServers": {}}
+
+    import threading
+
+    started_loop = asyncio.get_running_loop()
+    release_thread = threading.Event()
+    monkeypatch.setattr(personal_mcp, "_mutate", mutate)
+
+    task = asyncio.create_task(personal_mcp._write(SimpleNamespace(), "delete", "missing"))
+    try:
+        await asyncio.wait_for(started.wait(), timeout=5)
+        task.cancel()
+        await asyncio.sleep(0)
+        assert not task.done()
+
+        release_thread.set()
+        with pytest.raises(asyncio.CancelledError):
+            await task
+    finally:
+        release_thread.set()
+        if not task.done():
+            task.cancel()
+            await asyncio.gather(task, return_exceptions=True)
+
+
 def test_persistent_same_name_connections_are_owner_only(personal_client):
     client = personal_client
     assert client.get("/api/mcp/personal/config").status_code == 401