Cursor doesnt see workspace/project-level defined MCP servers

[alexcarv318 (Alex Ilchenko)]

Where does the bug appear (feature/product)?

Cursor IDE

Describe the Bug

I have this issue while working in a workspace with multiple projects imported.

Let’s say I have project_1 and project_2.
Inside of project_2 I define the mcp.json file like this:
/project_2/.cursor/mcp.json

With this content:

{
  "mcpServers": {
    "neo4j-mcp": {
      "url": "http://127.0.0.1:18805/mcp/"
    }
  }
}

It doesnt appear in Customize section of the Cursor settings, even with my project_2 selected. While User MCP connections appear and they work well. Moreover, it seems like the agent can’t access them as well.

Please check the screenshots attached as well, to understand better

Steps to Reproduce

Option 1

1. Create an mcp.json file inside one of your projects that was added to workspace
2. Define an MCP server there
3. Go to “Settings” → “Customize”
4. Select the same project in the dropdown at left below the “Search MCPs”

Screenshots / Screen Recordings

Operating System

MacOS

Version Information

Cursor Version: 3.15.6
VS Code Extension API: 1.128.0
Commit: a1f686545fd0ce8917bbd2449f733551a9bce420
Date: 2026-08-06T01:41:03.876Z
Layout: IDE
Build Type: Stable
Release Track: Default
Electron: 40.10.3
Chromium: 144.0.7559.236
Node.js: 24.15.0
V8: 14.4.258.32-electron.0
xterm.js: 6.1.0-beta.291
OS: Darwin arm64 25.5.0

Does this stop you from using Cursor

No - Cursor works, but with this issue

[deanrie]

Hey, thanks for the detailed report with screenshots and the version. It really helped us narrow this down quickly.

What you’re describing is reproducible. In a multi-root workspace (multiple projects in one window), project-level servers from .cursor/mcp.json in the second and later roots don’t show up in Customize under any scope, and the agent doesn’t connect to them. This isn’t something in your setup. Your mcp.json is correct. This is a known issue we’re tracking, and I can’t share an ETA yet.

For now, there are two workarounds:

1. Move the server to the user-level config ~/.cursor/mcp.json. There’s no approval gate there, it’ll be picked up right away and the agent will be able to use it. Example:

   {
     "mcpServers": {
       "neo4j-mcp": {
         "url": "http://127.0.0.1:18805/mcp/"
       }
     }
   }
   

2. If you want to keep it project-scoped, make project_2 the first folder in the workspace and open it once in a separate window (not as part of the workspace) so you can approve the server. After that, it should stay valid in the workspace window too.

I’ll post here once I have an update. Let me know if the workarounds don’t help.

[Bruno_Ferreira]

hey! is there any expectation here? this is pretty bad. I had a workspace with multiple mcps on each one and it was great having cursor aggregating those for me… and now nothing works

[Michal_Gadzinski]

Hello, please provide the LE if possible for this bug. It has a wide impact on general MCP usage.

[jsphbtst (Joseph)]

Seems like the regression doesn’t just apply to multi-root workspaces. Managed to replicate on my project. Note: web/ here does not have its own .cursor/folder.

[Aldi_Jakaria]

Has this been fixed yet? this is a very breaking bug

[deanrie]

No update on timing yet. This is an issue we’re tracking, and I’ll reply right here as soon as there’s any news. For now, the easiest workaround is to move the server to the user-level config at ~/.cursor/mcp.json. There’s no approval gate there, it gets picked up right away, and the agent can use it.

@jsphbtst thanks for the screenshots. I can see sample-mcp in .cursor/mcp.json at the project root, but it doesn’t show up in the Customize list, even though User and Plugin MCP do show up. To figure out if this is the same issue or a different one, can you confirm a couple things:

1. Are you opening a single project in a single-folder window, or is this a multi-root .code-workspace with multiple folders?
2. Your Cursor version Cursor Settings > bottom, or About.
3. Does sample-mcp actually connect to the agent and do tools get called in chat, or is it not there at all?

The main case in this thread is multi-root, where servers from the second and later folders don’t show up. If you’re on single-folder and it still doesn’t appear, that’s a different scenario, and the details above will help us separate it.

[Stephen_Reid]

@deanrie

1. Are you opening a single project in a single-folder window, or is this a multi-root .code-workspace with multiple folders?

I’m still having problems with a single-folder workspace on 3.16.17

[deanrie]

Hey @Stephen_Reid, thanks for the report. Just to confirm, what’s described earlier in this thread is a multi-root .code-workspace setup with multiple folders in one window, and that case is already fixed in recent releases.

Your case is a single-folder workspace, which is a different scenario. We’re aware of it and tracking it, but it’s not the same as the main issue in this thread. I can’t share an exact ETA yet.

Workaround for now: move the server to the user-level config at ~/.cursor/mcp.json. There’s no approval gate there, so it gets picked up right away and the agent can see it. Example:

{
  "mcpServers": {
    "your-mcp": {
      "url": "http://127.0.0.1:PORT/mcp/"
    }
  }
}

To avoid mixing your single-folder case with the multi-root one in this thread and to track it more accurately, please start a separate thread. In it, include:

• The exact layout, where .cursor/mcp.json lives relative to the root of the folder you opened.
• Your Cursor version, you mentioned 3.16.17, please include it in the new thread too.
• Whether the server shows up anywhere under Customize and whether its tools are called from chat, or if it’s not visible at all.

Drop the link to the new thread here and I’ll follow up.

[Colin]

The fix for this issue landed in v3.17!