Cursor cli doesn't work with jira mcp in headless mode

Support Bug Reports
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1

Where does the bug appear (feature/product)?

Cursor CLI

Describe the Bug

I am trying to read a jira story using jira mcp using the cursor cli in prompt mode. I added the allowList in the permisions and in the cli-config.json as per the docs.

but when I run the prompt, it fails saying User rejected the mcp call.

WHen I run the agent in the interactive mode, it asks me if I want to run the mcp or not. This happens even if I add /auto-run

when I run agent mcp list it says jira is ‘not approved’

when I run agent mcp approve jira it says jira is already approved

Steps to Reproduce

  1. add jira mcp with the necessary tokens
  2. run agent -p "read jira story PROJ-XXXX" --approve-mcps --trust ( --force mode is restricted)

Expected Behavior

It should automatically read the jira using the mcp tool because I have added ALL jira tools as blanket approval.

Operating System

Linux

Version Information

About Cursor CLI

CLI Version 2026.04.16-2d20146
Model Composer 2
Subscription Tier Enterprise
OS linux (x64)
Terminal unknown
Shell bash

Does this stop you from using Cursor

Yes - Cursor is unusable

4

For Enterprise users, the mcp was not allowed in the admin allowed list. Once that was done, the mcp call went through, otherwise, we had to manually approve the mcp.

8

Hi @Suraj_Patil

Glad you got this sorted. You’re right: on Enterprise plans, MCP servers need to be added to the team’s admin allowlist in the Enterprise dashboard settings before they can be used. This is a team-level policy that applies on top of the local per-project approval, which is why --approve-mcps alone wasn’t enough.

The confusing part where agent mcp list shows “not approved” but agent mcp approve says “already approved” is because those commands only see the local approval state, which is separate from the enterprise admin policy. Once the Jira MCP was added to the admin allowlist, both layers were satisfied.

For anyone else on an Enterprise team hitting this: check with your team admin to ensure the MCP server is included in the MCP Configuration section under Enterprise-Only Settings in the team dashboard.

9

it would be helpful if the docs mention this. The docs did not mention that for Enterprise the admins had to approve! I was going insane passing --approve-mcps and it didn’t work for a while.