MCP Tools Being Re-enabled

Where does the bug appear (feature/product)?

Cursor IDE

Describe the Bug

MCP tools are being re-enabled after having manually disabled them. This is extremely annoying as it often (1) puts me over the 40 tool limit (2) breaks Cursor’s built-in tools (like search). I only realize that all of my MCP tools are re-enabled when my agent start acting strange. I then need to go to settings and disable all of the ones I don’t want.

This is really annoying as it causes the agent’s functionality to degrade massively. It issues terminal commands for basic functionality, instead of using the built in search tools.

Note: I specifically do not want to entirely delete all of these tools as I want them configured and ready to use. For example, I’ll generally have the Figma MCP disabled until I’m doing FE work against an actual product design. I don’t want to have to manually re-configure Figma each time I need it. I just want to flip it on.

Steps to Reproduce

  1. Configure an MCP tool

  2. Disable the MCP tool

  3. Go do stuff*

  4. Come back to settings to find all of the disabled MCP tools re-enabled

I’m not entirely sure what “do stuff is”. Though, it seems to be associated with a Cursor-level state change. For example, switching projects, restarting my computer, upgrading Cursor, etc, etc, etc.

It’s also possible that these tools are enabled on a per-workspace or per-project basis, but that’s simply not obvious to me.

Expected Behavior

MCP tools do not automatically re-enable themselves.

Operating System

MacOS

Current Cursor Version (Menu → About Cursor → Copy)

Version: 1.4.5 (Universal)

Additional Information

I do not believe this is version specific. It’s been happening for a while and I’ve just gotten around to reporting it.

Does this stop you from using Cursor

Sometimes - I can sometimes use Cursor

Hey, thanks for the report. Yes, indeed, MCP servers are enabled for each workspace. However, if this is inconvenient, you can try creating a project-specific .cursor/mcp.json file that lists specific MCP servers.