[BUG] Custom local MCP server tools disabled in Cowork and Claude Code, but work in Claude Chat Desktop app

[tommy-gun]

Preflight Checklist

• I have searched existing issues and this hasn't been reported yet
• This is a single bug report (please file separate reports for different bugs)
• I am using the latest version of Claude Code

What's Wrong?

A custom local MCP server (self-hosted, running locally) works correctly in the Claude desktop Chat interface, but all its tools are non-functional in Cowork mode and Claude Code. The tools are recognized and appear in the tool list, but any invocation returns:

This tool has been disabled in your connector settings.

What Should Happen?

The local MCP connector should work across the Claude Desktop application if tools are allowed.

Error Messages/Logs

This tool has been disabled in your connector settings.

Steps to Reproduce

1. Set up a custom local MCP server running locally by adding into claude_desktop_config.json
2. Connect it to Claude — tools work correctly in the chat interface
3. Open the same MCP connection in Cowork mode or Claude Code
4. Attempt to call any tool from the MCP server
5. Observe the error

Claude Model

Sonnet (default)

Is this a regression?

Yes, this worked in a previous version

Last Working Version

No response

Claude Code Version

2.1.90

Platform

Anthropic API

Operating System

Windows

Terminal/Shell

Windows Terminal

Additional Information

No response

[github-actions]

Found 3 possible duplicate issues:

1. [BUG] Local stdio MCP server (sequential-thinking) still returns "disabled in connector settings" in Cowork mode despite working perfectly in Chat mode (macOS, Max plan) — #20377 not resolved #41206
2. [BUG] COWORK || Local / desktop MCP tools not exposed to claude cowork, all the tools work properly in claude chat #20377
3. [BUG] All local MCP server tools blocked by PreToolUse:Callback in Code mode #35436

This issue will be automatically closed as a duplicate in 3 days.

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🤖 Generated with Claude Code

[fabiotheta-art]

This is not a duplicate of #20377 (which was closed without a documented fix) or the other listed issues. The problem persists in the current version (2.1.92) on Windows with a Python stdio MCP server. The tool shows "This tool has been disabled in your connector settings" in Cowork mode only. The local server starts correctly (py kb_mcp.py), config is set in settings.json, and tools work fine in Claude Chat Desktop. Please keep this open and track it separately for Cowork + Windows.

[matiasojedam]

I've been dealing with this bug for several weeks now and I'm extremely frustrated with the lack of progress. This is a critical issue that has been directly impacting my work — I rely on MCP connector tools as a core part of my workflow, and being unable to use them in Cowork has cost me significant time and productivity.
I'm paying for a service that I literally cannot use to its full capacity. Every day this remains unresolved is another day I'm essentially paying for a broken product. This is not a minor inconvenience — it affects real work that needs to get done.
I understand software bugs happen, but weeks without a fix or even a clear ETA is unacceptable for a paid product. At minimum, I'd expect a workaround, a status update, or a timeline. The silence from the team on this thread is making things worse.
Please prioritize this. It's been too long.

[tommy-gun]

Partial solution was to add mcp server as MCPB package. In latest version Claude 1.2581.0 (f10398) 2026-04-14T17:16:40.000Z it looks it helps in Cowork mode, but Code mode (in desktop app) still can not use this MCP server

[VioletJet1728]

Confirming on macOS — same symptom, same root cause. Filed #41206 (marked invalid) with full repro using @modelcontextprotocol/server-sequential-thinking.

Environment: macOS (Apple Silicon), Claude Desktop v1.1.9493 (b58a0b), Max plan.

Works in Chat mode. In Cowork mode every call returns "This tool has been disabled in your connector settings." Server logs confirm the call is blocked at the Cowork PreToolUse hook before reaching the MCP server — the server never receives a tools/call request.

Reproduces on both Windows (OP) and macOS, with both custom and official MCP servers. Not platform- or server-specific.

[Daimon-Law]

Still hitting the same problem I filed in March — happens consistently in Cowork mode regardless of which MCP is involved. Same error every time: This tool has been disabled in your connector settings. My workaround, for anyone else landing here:

1. Mount the MCP server's folder into the Cowork session.
2. Have Claude read the .env directly so credentials never have to be pasted into chat.
3. Call the underlying REST API directly.

It's a rough kludge but seems to work for now. Detailed repro and context are in my earlier report here but I'm happy to provide more if the dev team wants it.