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If an MCP server is missing, first check which client and workspace it is configured for, then verify its approval and connection status. A server can be configured without being approved or connected, and it can connect successfully while still returning no tools. Diagnose those stages separately before reinstalling anything.
Start by identifying the client, scope, and transport
“Claude” can mean Claude Code or Claude Desktop; their controls differ. Also establish whether the server runs locally as a stdio process or is reached through a remote HTTP-based transport, and whether its configuration belongs to the current project or to your user account. These distinctions often explain why a server appears in one app but not another.
- Configured: the client has a server definition.
- Approved or enabled: the client is permitted to use it. Project-level servers may remain pending approval until you trust the project and approve the server.
- Connected: the client can communicate with the server.
- Discovered: the server has reported tools to the client.
These are separate states. A configured or connected label alone does not prove that the server is approved for the current workspace or that tool discovery succeeded.
Check the correct configuration location
| Client | Where to check | Useful status or tool check |
|---|---|---|
| Claude Code | Use its MCP controls; project-level servers can require project trust and approval. | claude mcp list, claude mcp get <name>, or /mcp |
| Claude Desktop | In chat, open “Add files, connectors, and more” and inspect connected servers and their available tools. | Use the Connectors menu; Claude Code commands do not apply. |
| VS Code | VS Code uses .vscode/mcp.json with a top-level servers object. Its portable format uses .mcp.json or ~/.copilot/mcp-config.json with mcpServers. |
Run MCP: List Servers. |
| Cursor | Project config: .cursor/mcp.json. Global config: ~/.cursor/mcp.json. |
agent mcp list and agent mcp list-tools <identifier> |
In VS Code, configuration and environment variables are resolved where the server actually starts. If you are using a remote window, a runtime or token installed only on your local machine may not be available in the remote environment.
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Confirm that the transport matches
A local stdio server must launch as a process in the client’s environment and communicate over standard input and output. A remote server instead depends on a reachable endpoint and the appropriate transport, authentication, and any required headers. Do not copy a server definition between clients without checking its schema and transport settings. In Claude Code, a remote url needs an explicit matching type; a URL without a type is treated as stdio.
If the server will not start or connect
For a local server, inspect the command and its launch environment. For a remote server, investigate the endpoint and authorization rather than repeatedly restarting a configuration that cannot authenticate.
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For a local stdio server
- Validate the configuration JSON and required fields.
- Confirm the command exists in the environment where the client launches it. Check arguments, working directory, file permissions, and required environment variables; use an absolute command path if the launch directory is uncertain.
- If Docker is involved, keep the process in the foreground rather than using detached mode so the client can communicate over its standard streams.
- Keep ordinary diagnostic messages off standard output. The MCP debugging guidance warns that stdout is used for protocol communication; send normal logs to stderr instead.
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- Check the URL, declared transport, network reachability, authentication or OAuth state, and required headers.
- Treat HTTP 401, 403, and other 4xx responses as signs to check authorization or configuration, not as reasons for endless retries.
- For remote HTTP connections, use server-side logs and HTTP or network inspection; client stderr capture is not available in the same way as for a local process.
Read the client’s status before changing settings
In Claude Code, claude mcp list, claude mcp get <name>, and /mcp expose status and details. Reported states can include connected, needs authentication, failed to connect, pending approval, rejected, and disabled. The list command reflects configuration decisions and may include states that do not represent a fresh connection attempt. WebSocket entries may need to be checked with claude mcp get or /mcp rather than the ordinary list output.
If it says connected but no tools appear
Connection and discovery are different steps. After connecting, a client requests capabilities such as tools/list. A server can be reachable while that request fails, returns an empty list, or produces a response the client cannot use.
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Check discovery in the same client
- Claude Code: inspect
/mcpand the server details. Its documentation says transient network or server errors during discovery are retried up to three times with short backoff; authentication errors, 4xx responses, and request timeouts are not retried. - VS Code: inspect the server output. If you changed the server’s tool list, run
MCP: Reset Cached Tools, then restart the server and check the list again. Automatic discovery from Claude Desktop, Cursor, and other supported apps is controlled bychat.mcp.discovery.enabled; discovery sources are off by default in the configuration reference. - Cursor: use
agent mcp list-tools <identifier>to check whether the server exposes tools. For a server that requires authentication, useagent mcp login <identifier>. - Claude Desktop: inspect the available tools under the Connectors menu.
If the server’s discovery response is empty or malformed, investigate the server implementation, protocol compatibility, and server-side logs. A successful connection indicator does not establish that tool discovery worked.
Use logs and the MCP Inspector to isolate the fault
Open the relevant client logs
- In VS Code, run
MCP: List Servers, select the server, and choose Show Output. - In Claude Desktop, check
~/Library/Logs/Claudeon macOS or%APPDATA%Claudelogson Windows. - In Claude Code, use
/mcporclaude mcp get <name>to inspect connection and server details. - After correcting the reported issue in VS Code, choose Restart Server and retry.
Review diagnostic output before sharing it: logs and exports can expose prompts, source code, file paths, tool inputs or outputs, and credentials. Redact sensitive material.
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Test the server independently
The MCP Inspector is an interactive, transport-agnostic way to test stdio and Streamable HTTP servers, including their tools, prompts, and resources. Use the result to narrow the problem:
- If the Inspector cannot connect or list expected tools, focus on the server, its environment, protocol compatibility, or remote endpoint.
- If the Inspector works but the target client does not, compare that client’s configuration format, authentication, trust or approval state, and execution environment.
Reconnect and verify the actual tool list
Once you have corrected a specific cause, reconnect or restart the server and check the tools again in the same client and workspace. In VS Code, use Restart Server; after a tool-list change, reset cached tools as well. Claude Code provides reconnection controls through /mcp, with available commands depending on version. Cursor CLI provides status and tool-list checks through agent mcp list and agent mcp list-tools <identifier>.
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After each attempt, re-check the status or log. Restarting cannot by itself fix invalid JSON, a missing runtime, blocked network access, expired credentials, or a server-side discovery bug.
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