MCP servers configured but agent cannot use their tools

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Hey, this is a known issue. MCP servers can show as connected in the UI, but the agent doesn’t pick up their tools right away, or at all in some sessions.

A few workarounds that have helped others:

  1. Toggle the MCP server off and on in Cursor Settings > Tools & MCP. This forces a re-init. Sometimes toggling any MCP triggers a refresh for all of them.

  2. Call out the MCP by name in your first message. Instead of “create a pull request,” try “Using the GitHub MCP, create a pull request for…” This can prompt the agent to discover the tools.

  3. Try project-level config instead of global ~/.cursor/mcp.json. Add a .cursor/mcp.json in your project root with the same config. Some users report better reliability with project-level setup.

  4. After toggling, start a fresh chat. Existing sessions might not pick up newly available tools.

A couple questions to help dig further:

  • What status does GitHub MCP show in Cursor Settings > Tools & MCP, green, yellow, or red?
  • Is it configured only in ~/.cursor/mcp.json, or also at the project level?

The team is aware of this and tracking it.

Related threads if helpful:

Let me know how it goes.

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