Project-level MCP config (.cursor/mcp.json) is not loaded when opening a multi-root .code-workspace file.
The same MCP server appears correctly when I open the folder that contains .cursor/mcp.json directly. When I open a .code-workspace that includes that folder (plus a second folder), the project MCP does not show up in Settings → MCPs. User/global MCPs still work in the workspace.
Steps to Reproduce
Create folder A with .cursor/mcp.json defining a project MCP server (HTTP MCP in my case: emcp-aurorasdp).
Create a .code-workspace with two folders: folder A as first root, and another folder B as second root.
Open folder A alone in Cursor → Settings → MCPs: project MCP appears and connects (e.g. 188 tools enabled).
Close and open the .code-workspace instead.
Go to Settings → MCPs again.
Result: the project MCP from folder A is missing / not connected. Only user-level MCPs appear.
Expected Behavior
Opening a multi-root .code-workspace should still load project MCP servers from .cursor/mcp.json in the workspace folder(s), at least from the first root folder that contains the config — same behavior as opening that folder directly.
Hey there!
Even in a multi-root .code-workspace, Cursor still reads .cursor/mcp.json from your folders, so emcp-aurorasdp is most likely still active - it’s the Settings → MCPs list that doesn’t surface project servers while a .code-workspace is open, so it only looks missing. Opening folder A directly is the workaround to see/toggle it for now. This isn’t intended behavior for multi-root, and we’ve let the team know.
One quick check to be sure: with the .code-workspace open, are emcp-aurorasdp’s tools actually usable in Agent chat? If yes, it’s purely the list hiding it; if no, tell me and I’ll dig in.
Thanks for confirming - you’re right, and sorry for the wrong steer earlier. In a multi-root .code-workspace the project server genuinely doesn’t connect, so its tools aren’t available in Agent chat - not just the Settings list hiding it, and nothing on your end. This is an issue we’re tracking.
To unblock now:
Open folder A directly (a single-folder window instead of the .code-workspace) - that’s where it connects and the tools load, as you saw.
Or move that server to your user-level ~/.cursor/mcp.json (Windows: %USERPROFILE%\.cursor\mcp.json). User-level servers still load in multi-root; the tradeoff is it’s then available in every project, not just this one.