MCP servers unavailable in agents window

Support Bug Reports
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1

Where does the bug appear (feature/product)?

Cursor IDE

Describe the Bug

Where does the bug appear?

  • Agents Window / Glass agent chat

Describe the Bug

User MCP servers configured in ~/.cursor/mcp.json show up correctly in Cursor Settings → Tools & MCP (Editor/IDE), but the Agents Window agent runtime only receives a tiny subset of MCP servers:

  • cursor-app-control
  • plugin-exa-exa (plugin)

All of my configured user MCP servers are invisible to the agent (confirmed by asking the agent which MCP servers it can see via GetMcpTools catalog). This makes paid MCP workflows (Obsidian, W&B, Zotero, paper search, PDF reader, AlphaXiv, etc.) unusable in the Agents UI even though they are configured and visible in Settings.

This matches other reports about Agents Window MCP parity gaps vs Editor Window.

Steps to Reproduce

  1. Configure multiple MCP servers in ~/.cursor/mcp.json (stdio + HTTP localhost servers).
  2. Confirm they appear/connected in Settings → Tools & MCP.
  3. Open Agents Window / Glass agent chat.
  4. Ask the agent which MCP servers it sees / call GetMcpTools catalog.
  5. Observe only built-in/plugin MCPs are available; user mcp.json servers are missing.

Expected Behavior

Agents Window should expose the same enabled user MCP servers as Settings / Editor agent chat.

Screenshots / Screen Recordings

[attach: Settings showing many MCP servers vs agent listing only 2]

Operating System

Linux

Version info

3.12.30

Does this stop you from using Cursor?

Yes — MCP-dependent workflows in Agents Window are broken; I have to fall back to Editor chat / workarounds.

Steps to Reproduce

  1. Configure multiple MCP servers in ~/.cursor/mcp.json (stdio + HTTP localhost servers).
  2. Confirm they appear/connected in Settings → Tools & MCP.
  3. Open Agents Window / Glass agent chat.
  4. Ask the agent which MCP servers it sees / call GetMcpTools catalog.
  5. Observe only built-in/plugin MCPs are available; user mcp.json servers are missing.

Operating System

Linux

Version Information

3.12.30

Additional Information

The cursor project is configured via an ssh connection and the mcp.json is at the remote machine’s root. IDE picks the mcp config up with no problem but agents window does not.

Does this stop you from using Cursor

Sometimes - I can sometimes use Cursor

5

Hey, thanks for the detailed report. This is a known limitation of the Agents Window when using Remote SSH. The Editor Window resolves the MCP config through the remote extension host, so it picks up servers from the remote ~/.cursor/mcp.json. But the Agents Window resolves the user MCP config relative to your local machine, so servers that live in the home config on the remote host don’t reach the agent. Only local built-in or plugin servers show up. I can’t share an ETA for a fix yet.

For now, here are a few workarounds:

  • For MCP-dependent workflows over SSH, use the chat in the Editor Window. The remote ~/.cursor/mcp.json works there.
  • Put the servers into .cursor/mcp.json inside the repo on the remote host. The workspace-scoped config is tied per workspace, and this helps re-bind MCP on the remote machine.
  • Servers that can run locally can be added to your local ~/.cursor/mcp.json. They’ll appear in the Agents Window. But stdio servers that need binaries on the remote host, and HTTP servers bound to the remote machine’s localhost, won’t work without port forwarding.

Related threads with the same issue: this one User MCP Servers in Agents Window are inconsistent with Editor Window when using Remote SSH and this one MCP breaks after switching between Cursor IDE and Agents window on the same WSL Remote workspace WSL. If there’s an update, I’ll post it here.