BUG: MCP servers fail to connect in Claude Code despite correct configuration

[GratefulDave]

Bug Description
Operating System: macOS Darwin 24.5.0

Node.js Version: v23.10.0 (via nvm)

Issue Description:
MCP servers consistently fail to connect in Claude Code, even though they are properly configured and the servers themselves work correctly when tested independently.

Steps to Reproduce:

1. Install MCP server globally:
   npm install -g @modelcontextprotocol/server-filesystem
2. Add MCP server to Claude Code:
   claude mcp add filesystem "npx" "@modelcontextprotocol/server-filesystem" "/Users/username/Projects/"
3. Verify server is listed:
   claude mcp list

Output shows: filesystem: npx @modelcontextprotocol/server-filesystem /Users/username/Projects/

4. Start Claude Code:
   claude
5. Attempt to use MCP tools - all fail with "MCP servers failed to connect"

Expected Behavior:
MCP servers should connect and be available for use within Claude Code.

Actual Behavior:
All MCP servers fail to connect, despite being properly configured and working when tested independently.

Additional Information:

1. The MCP server works correctly when tested directly:
   echo '{"jsonrpc":"2.0","method":"initialize","params":{"protocolVersion":"2024-11-05","clientInfo":{"name":"test","version":"1.0.0"},"capabilities":{}},"id":1}' | npx @modelcontextprotocol/server-filesystem /path/to/directory
2. Returns successful initialization response.
3. Tried multiple configuration approaches:
   - Using npx with -y flag
   - Using direct node path with full path to server
   - Creating .mcp.json in project directory
   - Using --mcp-config flag with JSON file
   - Importing from Claude Desktop config
4. No error logs are generated in any standard log locations.
5. The same configuration works in Claude Desktop app but fails in Claude Code CLI.

Environment Details:

• Multiple MCP servers tested (filesystem, memory, github, etc.)
• All exhibit the same connection failure
• No permission issues (all files have correct permissions)
• PATH includes node/npm directories

This appears to be a fundamental issue with Claude Code's MCP integration rather than a configuration problem, as the servers work correctly outside of Claude Code.

Environment Info

• Platform: macos
• Terminal: pycharm
• Version: 1.0.11
• Feedback ID: 74d37a8d-973a-43c3-96ea-e43aa60b7888

Errors

[{"error":"AbortError: The operation was aborted\n    at abortChildProcess (node:child_process:716:27)\n    at onAbortListener (node:child_process:786:7)\n    at process.processTicksAndRejections (node:internal/process/task_queues:85:11)","timestamp":"2025-06-04T23:03:51.295Z"},{"error":"Error: Command failed: security find-generic-password -a $USER -w -s \"Claude Code\"\nsecurity: SecKeychainSearchCopyNext: The specified item could not be found in the keychain.\n\n    at genericNodeError (node:internal/errors:983:15)\n    at wrappedFn (node:internal/errors:537:14)\n    at checkExecSyncError (node:child_process:882:11)\n    at execSync (node:child_process:954:15)\n    at JZ (file:///Users/davidandrews/.nvm/versions/node/v23.10.0/lib/node_modules/@anthropic-ai/claude-code/cli.js:683:2402)\n    at file:///Users/davidandrews/.nvm/versions/node/v23.10.0/lib/node_modules/@anthropic-ai/claude-code/cli.js:582:11763\n    at Q (file:///Users/davidandrews/.nvm/versions/node/v23.10.0/lib/node_modules/@anthropic-ai/claude-code/cli.js:526:17069)\n    at LU (file:///Users/davidandrews/.nvm/versions/node/v23.10.0/lib/node_modules/@anthropic-ai/claude-code/cli.js:582:10909)\n    at HG (file:///Users/davidandrews/.nvm/versions/node/v23.10.0/lib/node_modules/@anthropic-ai/claude-code/cli.js:582:10355)\n    at lO2 (file:///Users/davidandrews/.nvm/versions/node/v23.10.0/lib/node_modules/@anthropic-ai/claude-code/cli.js:2042:4758)","timestamp":"2025-06-04T23:03:51.321Z"},{"error":"Error: No logs found at /Users/davidandrews/Library/Caches/claude-cli-nodejs/-Users-davidandrews-PycharmProjects-lexgenius/messages\n    at tT4 (file:///Users/davidandrews/.nvm/versions/node/v23.10.0/lib/node_modules/@anthropic-ai/claude-code/cli.js:583:3738)\n    at iQ1 (file:///Users/davidandrews/.nvm/versions/node/v23.10.0/lib/node_modules/@anthropic-ai/claude-code/cli.js:583:3487)\n    at OAA.<anonymous> (file:///Users/davidandrews/.nvm/versions/node/v23.10.0/lib/node_modules/@anthropic-ai/claude-code/cli.js:2337:2015)\n    at process.processTicksAndRejections (node:internal/process/task_queues:105:5)\n    at async OAA.parseAsync (file:///Users/davidandrews/.nvm/versions/node/v23.10.0/lib/node_modules/@anthropic-ai/claude-code/cli.js:517:4184)\n    at async vE5 (file:///Users/davidandrews/.nvm/versions/node/v23.10.0/lib/node_modules/@anthropic-ai/claude-code/cli.js:2340:5983)\n    at async xE5 (file:///Users/davidandrews/.nvm/versions/node/v23.10.0/lib/node_modules/@anthropic-ai/claude-code/cli.js:2336:17530)","timestamp":"2025-06-04T23:03:51.349Z"},{"error":"AbortError: The operation was aborted\n    at abortChildProcess (node:child_process:716:27)\n    at AbortSignal.onAbortListener (node:child_process:786:7)\n    at [nodejs.internal.kHybridDispatch] (node:internal/event_target:827:20)\n    at AbortSignal.dispatchEvent (node:internal/event_target:762:26)\n    at runAbort (node:internal/abort_controller:449:10)\n    at abortSignal (node:internal/abort_controller:435:3)\n    at AbortController.abort (node:internal/abort_controller:468:5)\n    at Timeout._onTimeout (file:///Users/davidandrews/.nvm/versions/node/v23.10.0/lib/node_modules/@anthropic-ai/claude-code/cli.js:2336:15943)\n    at listOnTimeout (node:internal/timers:611:17)\n    at process.processTimers (node:internal/timers:546:7)","timestamp":"2025-06-04T23:03:54.232Z"},{"error":"ShellError: Shell command failed\n    at Object.call (file:///Users/davidandrews/.nvm/versions/node/v23.10.0/lib/node_modules/@anthropic-ai/claude-code/cli.js:1547:1326)\n    at process.processTicksAndRejections (node:internal/process/task_queues:105:5)\n    at async pZ5 (file:///Users/davidandrews/.nvm/versions/node/v23.10.0/lib/node_modules/@anthropic-ai/claude-code/cli.js:1889:19078)\n    at async YK1 (file:///Users/davidandrews/.nvm/versions/node/v23.10.0/lib/node_modules/@anthropic-ai/claude-code/cli.js:1889:17664)\n    at async dZ5 (file:///Users/davidandrews/.nvm/versions/node/v23.10.0/lib/node_modules/@anthropic-ai/claude-code/cli.js:1889:16706)\n    at async hZ5 (file:///Users/davidandrews/.nvm/versions/node/v23.10.0/lib/node_modules/@anthropic-ai/claude-code/cli.js:1889:16356)\n    at async oe (file:///Users/davidandrews/.nvm/versions/node/v23.10.0/lib/node_modules/@anthropic-ai/claude-code/cli.js:1889:15392)\n    at async oe (file:///Users/davidandrews/.nvm/versions/node/v23.10.0/lib/node_modules/@anthropic-ai/claude-code/cli.js:1889:16218)\n    at async oe (file:///Users/davidandrews/.nvm/versions/node/v23.10.0/lib/node_modules/@anthropic-ai/claude-code/cli.js:1889:16218)\n    at async oe (file:///Users/davidandrews/.nvm/versions/node/v23.10.0/lib/node_modules/@anthropic-ai/claude-code/cli.js:1889:16218)","timestamp":"2025-06-04T23:05:14.363Z"},{"error":"ShellError: Shell command failed\n    at Object.call (file:///Users/davidandrews/.nvm/versions/nod

Note: Error logs were truncated.

[afsheee]

was this fixed? i'm still having issues with claude code connecting to supabase mcp

[leaanthony]

Same issue for basically any mcp server

[banditFox]

Experiencing the same issue.
Restarting Claude several times and eventually it connects. But it's almost like the MCP server needs to be 'warmed up'?

A restart of claude, initiazes the app but page is blank. Go to settings, then closing settings, and then the page populates.

macOS: Sequoia 15.5
node version v22.16.0

UPDATE: Ok, folks. So some complexity here.

1. I had Node installed but npm was installed globally so npm --version would returned a 'not recognized'.
2. I did not have the location of npm.
3. Re-installed npm (kinda) and added the path to my ~.zshrc

I'm still testing, but so far seems like it's working much faster and bettah.

In short;

1. Make sure npm is running locally.
2. Make sure ~.zshrc has the 'export NVM_DIR="$HOME/ .nvm" in the config.
3. Shut down iTerm, shut-down Claude Desktop. and fire everything back up. Should work.

[vishwa-prabhath]

I have the same issue .I just had the demo server code in demo server python sdk . It also give me cant connect to the mcp server. Any suggestions?

[ashwin-ant]

Can you try running claude --debug to see if anything is displayed?

[vishwa-prabhath]

i tried to but i cant get to run claude debug .cli is not found and I dont think its the issue since im using python sdk.

[edbyford]

Having the same problem with a couple of MCP servers.

[pjgoodall]

wasted hours trying to get gitea MCP working with claude-code