diff --git a/projects/jupyter-server-ydoc/jupyter_server_ydoc/app.py b/projects/jupyter-server-ydoc/jupyter_server_ydoc/app.py
index eb995de0..34431443 100644
--- a/projects/jupyter-server-ydoc/jupyter_server_ydoc/app.py
+++ b/projects/jupyter-server-ydoc/jupyter_server_ydoc/app.py
@@ -229,11 +229,27 @@ async def get_document(
         return None
 
     async def stop_extension(self):
-        # Cancel tasks and clean up
-        await asyncio.wait(
+        self.log.info("Stopping collaboration extension...")
+        _, pending = await asyncio.wait(
             [
                 asyncio.create_task(self.ywebsocket_server.clean()),
                 asyncio.create_task(self.file_loaders.clear()),
             ],
             timeout=3,
         )
+        if pending:
+            self.log.warning(
+                "Collaboration shutdown: %d task(s) still pending after 3s timeout, cancelling.",
+                len(pending),
+            )
+            for task in pending:
+                task.cancel()
+            # Wait briefly for cancellation to propagate
+            _, still_pending = await asyncio.wait(pending, timeout=1)
+            if still_pending:
+                self.log.error(
+                    "Collaboration shutdown: %d task(s) could not be cancelled.",
+                    len(still_pending),
+                )
+        else:
+            self.log.info("Collaboration extension stopped cleanly.")
diff --git a/projects/jupyter-server-ydoc/jupyter_server_ydoc/handlers.py b/projects/jupyter-server-ydoc/jupyter_server_ydoc/handlers.py
index dab437c1..60c2431b 100644
--- a/projects/jupyter-server-ydoc/jupyter_server_ydoc/handlers.py
+++ b/projects/jupyter-server-ydoc/jupyter_server_ydoc/handlers.py
@@ -79,11 +79,14 @@ def create_task(self, aw):
         task = asyncio.create_task(aw)
         self._background_tasks.add(task)
         task.add_done_callback(self._background_tasks.discard)
+        return task
 
     async def prepare(self):
         await ensure_async(super().prepare())
+        if self._websocket_server.stopping:
+            raise web.HTTPError(503, "Server is shutting down")
         if not self._websocket_server.started.is_set():
-            self.create_task(self._websocket_server.start())
+            self._websocket_server._start_task = self.create_task(self._websocket_server.start())
             await self._websocket_server.started.wait()
 
         # Get room
diff --git a/projects/jupyter-server-ydoc/jupyter_server_ydoc/websocketserver.py b/projects/jupyter-server-ydoc/jupyter_server_ydoc/websocketserver.py
index 13fb5375..48fb37a6 100644
--- a/projects/jupyter-server-ydoc/jupyter_server_ydoc/websocketserver.py
+++ b/projects/jupyter-server-ydoc/jupyter_server_ydoc/websocketserver.py
@@ -56,28 +56,35 @@ def __init__(
         self.connected_users: dict[Any, Any] = {}
         # Async loop is not yet ready at the object instantiation
         self.monitor_task: asyncio.Task | None = None
+        self._stopping = False
+        self._start_task: asyncio.Task | None = None
+
+    @property
+    def stopping(self) -> bool:
+        return self._stopping
 
     async def clean(self):
         # TODO: should we wait for any save task?
-        self.log.info("Deleting all rooms.")
         # FIXME some clean up should be upstreamed and the following does not
         # prevent hanging stop process - it also requires some thinking about
         # should the ystore write action be cancelled; I guess not as it could
         # results in corrupted data.
-        # room_tasks = list()
-        # for name, room in list(self.rooms.items()):
-        #     for task in room.background_tasks:
-        #         task.cancel()  # FIXME should be upstreamed
-        #         room_tasks.append(task)
-        # if room_tasks:
-        #     _, pending = await asyncio.wait(room_tasks, timeout=3)
-        #     if pending:
-        #         msg = f"{len(pending)} room task(s) are pending."
-        #         self.log.warning(msg)
-        #         self.log.debug("Pending tasks: %r", pending)
-
-        await self.stop()
-        tasks = []
+        self.log.info("Cleaning up %d room(s).", len(self.rooms))
+        # Reject new WebSocket connections in YDocWebSocketHandler.prepare().
+        self._stopping = True
+
+        # Stop the server first to reject any new connections during shutdown.
+        # Guard: stop() raises RuntimeError if the server was never started.
+        if self.started.is_set():
+            await self.stop()
+
+        # Now disconnect existing clients so their serve() tasks complete.
+        tasks: list[asyncio.Task] = []
+        for room in self.rooms.values():
+            for client in list(room.clients):
+                tasks.extend(client._background_tasks)  # type: ignore[attr-defined]
+                client._message_queue.put_nowait(b"")  # type: ignore[attr-defined]
+
         if self.monitor_task is not None:
             self.monitor_task.cancel()
             tasks.append(self.monitor_task)
@@ -85,9 +92,29 @@ async def clean(self):
         if tasks:
             _, pending = await asyncio.wait(tasks, timeout=3)
             if pending:
-                msg = f"{len(pending)} task(s) are pending."
-                self.log.warning(msg)
-                self.log.debug("Pending tasks: %r", pending)
+                self.log.warning("%d task(s) still pending after shutdown.", len(pending))
+
+        # Rooms persist after client disconnect so users can reconnect without
+        # a full re-sync (see auto_clean_rooms=False in app.py). On shutdown
+        # we must stop them explicitly.
+        for room in self.rooms.values():
+            try:
+                await room.stop()
+            except RuntimeError as e:
+                if "not running" not in str(e):
+                    raise
+        self.rooms.clear()
+
+        # Await the root asyncio task so anyio's task group __aexit__ runs
+        # and fires done-callbacks that clean up worker threads. Without this,
+        # non-daemon WorkerThread instances block Python's threading._shutdown().
+        if self._start_task is not None and not self._start_task.done():
+            try:
+                await asyncio.wait_for(self._start_task, timeout=2)
+            except asyncio.TimeoutError:
+                # Letting this propagate would be silently swallowed by
+                # asyncio.wait() in stop_extension(), so we log it here.
+                self.log.warning("Server start task did not complete within 2s.")
 
     def room_exists(self, path: str) -> bool:
         """