diff --git a/navi/main.py b/navi/main.py
index 080a7fd..2e0b849 100644
--- a/navi/main.py
+++ b/navi/main.py
@@ -133,6 +133,8 @@
     if _mcp_manager is not None:
         try:
             await _mcp_manager.disconnect_all()
+        except (asyncio.CancelledError, RuntimeError):
+            pass
         except Exception:
             pass
 
diff --git a/navi/mcp/client.py b/navi/mcp/client.py
index 78191c8..d0f42cc 100644
--- a/navi/mcp/client.py
+++ b/navi/mcp/client.py
@@ -92,7 +92,12 @@
         """Close transport and reset state."""
         if not self._connected:
             return
-        await self._cleanup()
+        try:
+            await self._cleanup()
+        except (asyncio.CancelledError, RuntimeError):
+            # Graceful shutdown during app teardown — SSE transport teardown
+            # throws CancelledError / RuntimeError from anyio task scopes.
+            pass
 
     async def _cleanup(self) -> None:
         try:
diff --git a/navi/mcp/manager.py b/navi/mcp/manager.py
index 6ab1603..e52af03 100644
--- a/navi/mcp/manager.py
+++ b/navi/mcp/manager.py
@@ -59,13 +59,17 @@
         """Close every open connection and clear the client pool."""
         if not self._clients:
             return
-        results = await asyncio.gather(
-            *[c.disconnect() for c in self._clients.values()],
-            return_exceptions=True,
-        )
-        for name, exc in zip(self._clients, results):
-            if isinstance(exc, Exception):
-                logger.warning("MCP server %r disconnect error: %s", name, exc)
+        try:
+            results = await asyncio.gather(
+                *[c.disconnect() for c in self._clients.values()],
+                return_exceptions=True,
+            )
+            for name, exc in zip(self._clients, results):
+                if isinstance(exc, Exception):
+                    logger.warning("MCP server %r disconnect error: %s", name, exc)
+        except (asyncio.CancelledError, RuntimeError):
+            # Shutdown-time cancellation from anyio task scopes — safe to ignore
+            pass
         self._clients.clear()
 
     async def get_all_tools(self) -> list[tuple[str, Any]]: