Claude Code Rovo MCP API Token Authentication

[zach_morgan]

Hi,

My atlassian admin and I are struggling to get our workflow working using the Atlassian Rovo MCP with API Token authentication. We are trying to put an automated process in place through our CI/CD pipeline to generate Jira tickets. We have configured everything based on the docs (https://support.atlassian.com/security-and-access-policies/docs/manage-atlassian-rovo-mcp-server/). However, when we connect, the only "tools" available for claude to use are to readonly ones. I am getting this error:

Unfortunately, I'm unable to create a Jira ticket. The Atlassian MCP tools available to me (`getTeamworkGraphContext` and `getTeamworkGraphObject`) are **read-only** — they can fetch and display existing Jira data but cannot create new issues. The attempt to access the Atlassian API also returned a 401 Unauthorized error, which suggests the MCP integration may not be fully configured with write permissions.

I have tried three different API tokens all having full permissions. I've tried removing the mcp connection and putting it back. Nothing seems to get it to have access to any other tools/permissions. We are stuck at this point.

This is our mcp configuration

{"mcpServers":{"atlassian":{"type":"http","url":"https://mcp.atlassian.com/v1/mcp","headers":{"Authorization":"Bearer ${{ secrets.ATLASSIAN_MCP_API_TOKEN }}"}}}}

[Dr Valeri Colon _Connect Centric_ · Accepted solution]

Good catch @zach_morgan —this is a common gotcha. Rovo MCP doesn’t currently support Bearer token auth for this setup, so it falls back to read-only tools. That’s why you only saw getTeamworkGraph methods. Switching to Basic auth (email + API token) enables full access, including write operations like creating Jira issues. If you see read-only tools, it’s usually an auth method issue, not permissions.

[Sumit Mahajan]

@Dr Valeri Colon _Connect Centric_ Im using auth token i can able to access tools list but not able to call tools using token i have also check the token expiry. 

[Dr Valeri Colon _Connect Centric_]

@Sumit Mahajan  if you can see the tools but can’t call them, that usually points to auth format or permission scope, not token expiry. Make sure you’re using Basic auth (email + API token), not Bearer. Also check:

• the user tied to the token has Jira permissions to create issues
• MCP is enabled for your org/site

If those are correct, it may be a tool execution limitation or MCP issue—worth raising with Atlassian support.

[zach_morgan]

Figured it out. Needed Basic auth not Bearer token: Followed this: https://www.builder.io/blog/claude-code-with-jira