diff --git a/backend/app/gateway/routers/subagents.py b/backend/app/gateway/routers/subagents.py
index 35c0bb6436..421e5c5e77 100644
--- a/backend/app/gateway/routers/subagents.py
+++ b/backend/app/gateway/routers/subagents.py
@@ -3,6 +3,7 @@
 from __future__ import annotations
 
 import asyncio
+from collections.abc import Callable
 from typing import Any, Literal
 
 from fastapi import APIRouter, HTTPException, Request
@@ -20,6 +21,7 @@ from deerflow.persistence.managed_subagents.base import (
     normalize_managed_subagent_name,
 )
 from deerflow.subagents.builtins import BUILTIN_SUBAGENTS
+from deerflow.utils.file_io import await_drained
 
 router = APIRouter(prefix="/api/subagents", tags=["subagents"])
 _ADMIN_REQUIRED_DETAIL = "Admin privileges are required to manage subagents."
@@ -74,6 +76,11 @@ class ManagedSubagentUpdateRequest(BaseModel):
     enabled: bool | None = None
 
 
+async def _run_store_mutation[**P, T](func: Callable[P, T], /, *args: P.args, **kwargs: P.kwargs) -> T:
+    """Drain persistent managed-subagent writes before cancellation propagates."""
+    return await await_drained(asyncio.to_thread(func, *args, **kwargs))
+
+
 def _validate_model(model: str, app_config) -> None:
     if model == "inherit":
         return
@@ -180,7 +187,7 @@ async def create_managed_subagent(request: Request, body: ManagedSubagentCreateR
         raise HTTPException(status_code=409, detail=f"Subagent name '{definition.name}' is reserved by a built-in or config.yaml definition.")
     store = get_managed_subagent_store(app_config)
     try:
-        await asyncio.to_thread(store.create, definition)
+        await _run_store_mutation(store.create, definition)
     except ManagedSubagentExistsError:
         raise HTTPException(status_code=409, detail=f"Managed subagent '{definition.name}' already exists")
     return SubagentResponse(
@@ -211,7 +218,7 @@ async def update_managed_subagent(name: str, request: Request, body: ManagedSuba
         raise HTTPException(status_code=422, detail=exc.errors()) from exc
     _validate_model(updated.model, app_config)
     try:
-        await asyncio.to_thread(store.update, updated)
+        await _run_store_mutation(store.update, updated)
     except FileNotFoundError:
         # The definition may be deleted by another administrator after the
         # read above. Preserve the endpoint's not-found contract instead of
@@ -234,5 +241,5 @@ async def delete_managed_subagent(name: str, request: Request) -> None:
     name = _validate_path_name(name)
     app_config = await asyncio.to_thread(get_app_config)
     store = get_managed_subagent_store(app_config)
-    if not await asyncio.to_thread(store.delete, name):
+    if not await _run_store_mutation(store.delete, name):
         raise HTTPException(status_code=404, detail=f"Managed subagent '{name}' not found")
diff --git a/backend/tests/test_subagents_router.py b/backend/tests/test_subagents_router.py
index 40f48ea08f..9017d1fed9 100644
--- a/backend/tests/test_subagents_router.py
+++ b/backend/tests/test_subagents_router.py
@@ -2,6 +2,8 @@
 
 from __future__ import annotations
 
+import asyncio
+import threading
 from types import SimpleNamespace
 
 import pytest
@@ -31,6 +33,103 @@ def _environment(tmp_path, monkeypatch):
     reset_app_config()
 
 
+@pytest.mark.parametrize("operation", ["create", "update", "delete"])
+async def test_managed_subagent_writes_route_through_mutation_drain(monkeypatch, operation):
+    definition = router.ManagedSubagentDefinition(
+        name="planner",
+        description="Plans work",
+        system_prompt="Plan the work.",
+    )
+
+    class Store:
+        def create(self, value):
+            return value
+
+        def get(self, name):
+            assert name == "planner"
+            return definition
+
+        def update(self, value):
+            return value
+
+        def delete(self, name):
+            assert name == "planner"
+            return True
+
+    store = Store()
+    calls: list[tuple[object, tuple[object, ...]]] = []
+
+    async def drained(func, /, *args, **kwargs):
+        calls.append((func, args))
+        return func(*args, **kwargs)
+
+    monkeypatch.setattr(router, "get_managed_subagent_store", lambda *_: store)
+    monkeypatch.setattr(router, "_run_store_mutation", drained)
+
+    if operation == "create":
+        await router.create_managed_subagent(
+            _request("admin"),
+            router.ManagedSubagentCreateRequest(
+                name="planner",
+                description="Plans work",
+                system_prompt="Plan the work.",
+            ),
+        )
+        expected = store.create
+    elif operation == "update":
+        await router.update_managed_subagent(
+            "planner",
+            _request("admin"),
+            router.ManagedSubagentUpdateRequest(enabled=False),
+        )
+        expected = store.update
+    else:
+        await router.delete_managed_subagent("planner", _request("admin"))
+        expected = store.delete
+
+    assert len(calls) == 1
+    assert calls[0][0] == expected
+
+
+async def test_create_managed_subagent_drains_started_write_across_repeated_cancellation(monkeypatch):
+    started = threading.Event()
+    release = threading.Event()
+
+    class Store:
+        def create(self, _definition):
+            started.set()
+            assert release.wait(timeout=2)
+
+    monkeypatch.setattr(router, "get_managed_subagent_store", lambda *_: Store())
+
+    task = asyncio.create_task(
+        router.create_managed_subagent(
+            _request("admin"),
+            router.ManagedSubagentCreateRequest(
+                name="planner",
+                description="Plans work",
+                system_prompt="Plan the work.",
+            ),
+        )
+    )
+    try:
+        assert await asyncio.to_thread(started.wait, 2)
+        task.cancel()
+        await asyncio.sleep(0.05)
+        task.cancel()
+        await asyncio.sleep(0.05)
+        assert not task.done()
+
+        release.set()
+        with pytest.raises(asyncio.CancelledError):
+            await task
+    finally:
+        release.set()
+        if not task.done():
+            task.cancel()
+            await asyncio.gather(task, return_exceptions=True)
+
+
 async def test_admin_can_create_update_and_delete_managed_subagent():
     created = await router.create_managed_subagent(
         _request("admin"),