MCP server connected in UI but tools not available to Agent runtime

Where does the bug appear (feature/product)?

Cursor IDE

Describe the Bug

prod-mysql-ssh shows connected in Settings → Tools & MCP (200+ table resources load), but Agent cannot call its tools. Persists across 3+ new chats and reload.

Steps to Reproduce

Configure prod-mysql-ssh in ~/.cursor/mcp.json
Open ai-engine-asana workspace
Confirm server connected in Tools & MCP
New Agent chat → ask agent to run SELECT 1 via mysql_query

Expected Behavior

Agent registers user-prod-mysql-ssh and can call mysql_query

Screenshots / Screen Recordings

Operating System

MacOS

Version Information

Cursor 3.7.42
macOS 26.5.1

For AI issues: which model did you use?

Auto

For AI issues: add Request ID with privacy disabled

35e8b54f-2620-4af3-b628-3bea47cecbb7
47c45feb-7713-4066-862b-3a2d1f4986fa

Does this stop you from using Cursor

Yes - Cursor is unusable

Hey, thanks for the detailed report. This is a known bug: the server shows as Connected and the resources load, but its tools don’t reach the agent because of a race when pushing the tool snapshot. Reload by itself usually doesn’t help.

The workaround is to toggle, not reload:

  • Open Settings → Tools & MCP
  • Turn off the prod-mysql-ssh toggle
  • Turn it back on
  • Open a new Agent chat and try mysql_query again

This forces a fresh tools snapshot, and the agent should see the tools. Having 200+ resources on the server isn’t the cause.

We’re tracking the bug, but I can’t share an exact ETA for the fix yet. If the toggle doesn’t help, let me know and we’ll dig deeper.

I have already tried all the steps mentioned still it is not working.

Hey, sorry the toggle didn’t fix it. Since the server is over SSH stdio, the connection can take a bit, and the Agent may take a snapshot of tools before the server has time to send them. Let’s check a couple things:

  1. Fully close Cursor Quit, not just reload the window, then open it again.
  2. Wait until prod-mysql-ssh turns green in Settings → Tools & MCP, and make sure it shows a tool count under it like mysql_query, not 0 tools.
  3. Only then open a new Agent chat and try calling mysql_query.

If it still can’t see it, can you share:

  • What the UI shows under the server, does it show a tool count or 0 tools?
  • MCP logs: open the Output panel via View → Output, pick MCP logs in the dropdown, and paste what shows up when prod-mysql-ssh connects.

That’ll help us tell if the tools are reaching the client at all, or if it’s only the Agent snapshot that’s getting blocked.