Cloud Agents triggered from Jira can't read/write Jira

[Msusu]

Where does the bug appear (feature/product)?

Background Agent (GitHub, Slack, Web, Linear)

Describe the Bug

There is an asymmetry between Cursor’s Jira integration and the Cloud Agent runtime it triggers:

The Jira ↔ Cursor integration has working write access to our Jira tenant — it successfully posts a comment back to the originating ticket when the Cloud Agent completes.
The Cloud Agent itself, spawned by that same trigger, reports the Atlassian MCP server as needsAuth and exposes zero Jira tools. It cannot read the originating ticket, search related issues, edit descriptions, or create child tickets — even though the platform around it clearly holds credentials for that exact tenant.
There is also no surfaced way to authenticate the Atlassian MCP for Cloud Agents from the dashboard. The Edit MCP server dialog only accepts URL / headers / Client ID / Client Secret; no Connect / Sign in affordance exists on the row, so the OAuth flow that exists on Desktop cannot be triggered for the Cloud Agent runtime.

In Cursor Desktop, the same Atlassian MCP against the same Atlassian Cloud tenant is fully authenticated (green status, Logout button, 31 tools / 4 resources). Desktop auth does not propagate to Cloud Agents.

Steps to Reproduce

1. In the Cursor dashboard → Integrations, connect:
   Jira → Status: Connected: Jira
   Jira Personal Account → Status: Your Jira account is linked to Cursor
2. In the Cursor dashboard → Team MCP Servers, add:
   “Atlassian-MCP-Server”: {
   “url”: “https://mcp.atlassian.com/v1/mcp/authv2”
   }
3. Trigger a Cloud Agent from a Jira ticket via the integration.
4. Inside the agent run, inspect the MCP servers — Atlassian-MCP-Server reports serverStatus: needsAuth and exposes no tools.
5. Ask the agent to read the originating Jira ticket — it cannot, and reports no Jira tools are available.
6. The agent completes, and Cursor’s backend still successfully posts a comment back to the same Jira ticket (proving the platform has the credentials).
   7.. Return to the dashboard’s Edit MCP server dialog for Atlassian-MCP-Server — there is no Connect / Sign in control to complete OAuth for the Cloud Agent runtime.

Expected Behavior

Either:

The credentials held by the Jira integration are made available to the MCP layer of any Cloud Agent it spawns, or
The dashboard exposes an explicit OAuth flow for the Atlassian MCP that uses the https://www.cursor.com/agents/mcp/oauth/callback callback and persists the resulting token at team/user scope so Cloud Agents inherit it on startup.
In both cases, a Cloud Agent triggered from a Jira ticket should be able to:

Read the originating ticket (getJiraIssue).
Edit the ticket description (editJiraIssue) — e.g. to append a tech-refinement brief after cross-checking requirements against the codebase.
Create properly-linked child or sibling tickets (createJiraIssue + createIssueLink) — e.g. to split off prerequisites or follow-ups discovered during analysis.

Operating System

Windows 10/11

Version Information

n.a. it is for cloud agent

Does this stop you from using Cursor

No - Cursor works, but with this issue

[Colin]

Hey @Msusu

You can authenticate your Atlassian MCP server from https://cursor.com/agents!

You can also decide to set up authentication with an API token if you don’t want individual users to need to authenticate. See the Atlassian docs here.

[Msusu]

So simple, thanks