I have lots of working MCP servers defined in my project’s mcp.json file but when I go to Cursor Settings → Customize → select repo within project → MCPs, the list is empty, no servers shown. I can’t see their status, can’t enable/disable them, and I can’t configure which tools are enabled/disabled. When I click on the “+New” button, it opens my mcp.json file and all my servers are there. And they work.
Steps to Reproduce
Make a multi-root workspace and add an mcp.json file.
Expected Behavior
All my custom MCP servers show up in the workspace level area and I can see their status and enable/disable them and their tools.
Same issue. Driving me nuts. Yesterday I was able to just go into settings and enable/disable my project level mcps. Now that’s apparently gone and there’s a “Customize” section. Except it’s for team, users, etc. My MCP’s are setup on a project by project basis, not on a user or team basis. They are often specific to projects (like test devices).
Anyone have any idea why they are doing this? What was broken that they are trying to fix and is there an official way to get them to look at it?
I need my MCP’s running
Edit: After typing this I went back in clicked on my username and I had workspace ones there. Seems to be working again.
Hey there!
Nothing’s wrong with your config, and those servers are still loaded and working. What you’re hitting is a scoping issue in the new Customize area specific to multi-root workspaces (a .code-workspace with more than one folder). It’s not intended behavior, and it’s an issue we’re tracking.
In the meantime, open the repo on its own (File → Open Folder → the repo root). In a single-folder window, Customize → MCPs lists that repo’s servers with status and enable/disable toggles. You can also keep editing them directly in .cursor/mcp.json (what “+ New” opens).
Five days and this issue is still open. I have so many problems with the multi-root workspace in Cursor that I think the company is trying to push me towards competing solutions.
@mohitjain still reproducing on 3.16.13 Nightly (Aug 13 build), macOS arm64.
My setup: multi-root workspace with 4 folders. 2 user servers in ~/.cursor/mcp.json, 10 project servers across three of the folders (1 + 5 + 4). Customize > MCPs shows “Connected 2” with only the user servers, under every scope in the dropdown. The project servers are connected and the agent calls their tools fine, so it’s only the UI.
One detail I haven’t seen in this thread yet: the scope dropdown itself is incomplete. It offers only 2 of my 4 folders. The folder with the most config (4 MCP servers plus rules and skills) never appears as an option at all, so even the “select the owning folder” path is dead for it. It’s not just server rows being filtered out, folders are missing from the scope picker too.
This is quite a bad regression, imho. MCP servers are core to the whole Cursor experience. Not testing how this new setup works in multi-root workspaces is not a great look.
Nothing’s wrong with your config, and those servers are still loaded and working
This is false. My agent reports that it sees no MCP servers. This is in version 3.15.19.
…
Just tested with Nightly (3.16.13). At least that version uses the project MCP servers again, even though the UI still doesn’t show them.
This is much much worse: it literally blocks all MCP usage in Cursor.
All our MCPs require authentication - this is obvious, since MCPs are handling critical data.
The new system makes it literally impsosible to authenticate any MCP server - you removed the UI that would show a button ‘authenticate’. There is no workaround as far as I can see.
