MCP servers are configured in Cursor, but their tools are not available to the agent in Composer. For example, GitHub MCP is set up in ~/.cursor/mcp.json, but the agent cannot use tools like create_pull_request, get_repository, etc. The agent only has access to built-in tools (Shell, Read, Write, Grep, etc.), not the MCP tools. This happens even after restarting Cursor and starting new sessions.
Steps to Reproduce
Add an MCP server in Cursor (e.g., GitHub) via Settings → Features → MCP or ~/.cursor/mcp.json.
Confirm the server is listed and enabled in MCP settings.
Open Composer and start a new agent session.
Ask the agent to perform an MCP-specific task (e.g., create a pull request or list issues).
Observe that the agent reports it does not have access to MCP tools and only uses built-in tools.
Expected Behavior
The agent should be able to use tools exposed by configured MCP servers (e.g., GitHub, Shopify dev MCP). When an MCP server is enabled, its tools should appear in the agent’s tool list and be callable during the session.
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:
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.
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.
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.
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?
Toggling the MCP server off and back on in Cursor Settings → Tools & MCP did the trick. It seems like this sometimes happens after Cursor auto-updates to a newer version. When that happens, I just need to toggle the MCP server to get everything working again.
also, yes all my mcps are configured in ~/.cursor/mcp.json
