diff --git a/packages/core/src/agents/local-executor.ts b/packages/core/src/agents/local-executor.ts
index 2302e117f8..0c8e55ad65 100644
--- a/packages/core/src/agents/local-executor.ts
+++ b/packages/core/src/agents/local-executor.ts
@@ -625,6 +625,15 @@ export class LocalAgentExecutor<TOutput extends z.ZodTypeAny> {
         }
       } finally {
         this.config.userHintService.offUserHint(hintListener);
+
+        const globalMcpManager = this.context.config.getMcpClientManager();
+        if (globalMcpManager) {
+          globalMcpManager.removeRegistries({
+            toolRegistry: this.toolRegistry,
+            promptRegistry: this.promptRegistry,
+            resourceRegistry: this.resourceRegistry,
+          });
+        }
       }
 
       // === UNIFIED RECOVERY BLOCK ===
diff --git a/packages/core/src/tools/mcp-client-manager.ts b/packages/core/src/tools/mcp-client-manager.ts
index 2f208c70d7..a607b19508 100644
--- a/packages/core/src/tools/mcp-client-manager.ts
+++ b/packages/core/src/tools/mcp-client-manager.ts
@@ -164,6 +164,16 @@ export class McpClientManager {
     return this.clients.get(serverName);
   }
 
+  removeRegistries(registries: {
+    toolRegistry: ToolRegistry;
+    promptRegistry: PromptRegistry;
+    resourceRegistry: ResourceRegistry;
+  }): void {
+    for (const client of this.clients.values()) {
+      client.removeRegistries(registries);
+    }
+  }
+
   /**
    * For all the MCP servers associated with this extension:
    *
diff --git a/packages/core/src/tools/mcp-client.ts b/packages/core/src/tools/mcp-client.ts
index 23d83f494a..58b7b6c8e2 100644
--- a/packages/core/src/tools/mcp-client.ts
+++ b/packages/core/src/tools/mcp-client.ts
@@ -266,6 +266,14 @@ export class McpClient implements McpProgressReporter {
     }
   }
 
+  /**
+   * Unregisters registries so this client will no longer update them when it receives
+   * list_changed notifications from the server.
+   */
+  removeRegistries(registries: RegistrySet): void {
+    this.registeredRegistries.delete(registries);
+  }
+
   /**
    * Disconnects from the MCP server.
    */