Cursor agent cannot see custom MCP servers
In Cursor 3.9.8 on macOS, custom appear connected in settings but are not available to the chat agent. Servers listed in `~/.cursor/mcp.json` show as enabled with a green status in Tools & , and their tools are visible there. When the chat agent is asked to use one of those tools, it says the server does not exist.
The only servers the agent lists as available are plugin-based such as `context7`. Restarting Cursor, reloading the window, starting new chats, toggling the server, and removing and adding it again did not change anything. The servers run correctly on their own and expose their tools, so the likely issue is that Cursor launches them for settings but does not pass them into the actual chat agent session.
The project MCP descriptor folder also only shows plugin-based servers, while the `mcp.json` stdio servers are missing.
Key points
- Cursor 3.9.8 on macOS shows custom in settings but not in agent chat.
- The custom servers are defined in `~/.cursor/mcp.json` and appear enabled in Tools & .
- The chat agent only sees plugin-based such as `context7`.
- Restarting, reloading, new chats, toggling, and re-adding servers did not fix it.
- The servers work standalone, so the failure seems to be inside Cursor’s agent registration flow.