diff --git a/src/everything/server/index.ts b/src/everything/server/index.ts
index 7ee3eed9..f1459cc8 100644
--- a/src/everything/server/index.ts
+++ b/src/everything/server/index.ts
@@ -40,6 +40,8 @@ export const createServer: () => ServerFactoryResponse = () => {
   const taskStore = new InMemoryTaskStore();
   const taskMessageQueue = new InMemoryTaskMessageQueue();
 
+  let initializeTimeout: NodeJS.Timeout | null = null;
+
   // Create the server
   const server = new McpServer(
     {
@@ -98,7 +100,7 @@ export const createServer: () => ServerFactoryResponse = () => {
     // This is delayed until after the `notifications/initialized` handler finishes,
     // otherwise, the request gets lost.
     const sessionId = server.server.transport?.sessionId;
-    setTimeout(() => syncRoots(server, sessionId), 350);
+    initializeTimeout = setTimeout(() => syncRoots(server, sessionId), 350);
   };
 
   // Return the ServerFactoryResponse
@@ -110,6 +112,7 @@ export const createServer: () => ServerFactoryResponse = () => {
       stopSimulatedResourceUpdates(sessionId);
       // Clean up task store timers
       taskStore.cleanup();
+      if (initializeTimeout) clearTimeout(initializeTimeout);
     },
   } satisfies ServerFactoryResponse;
 };
diff --git a/src/everything/server/roots.ts b/src/everything/server/roots.ts
index 999fda13..34b12b21 100644
--- a/src/everything/server/roots.ts
+++ b/src/everything/server/roots.ts
@@ -63,15 +63,10 @@ export const syncRoots = async (server: McpServer, sessionId?: string) => {
           );
         }
       } catch (error) {
-        await server.sendLoggingMessage(
-          {
-            level: "error",
-            logger: "everything-server",
-            data: `Failed to request roots from client: ${
-              error instanceof Error ? error.message : String(error)
-            }`,
-          },
-          sessionId
+        console.error(
+          `Failed to request roots from client ${sessionId}: ${
+            error instanceof Error ? error.message : String(error)
+          }`
         );
       }
     };