Rovo Agent: GitHub MCP Authentication Error in Slack

[Vladyslav Berezhetskyi]

Hello everyone,

I’ve created a Rovo Agent in Atlassian Studio and integrated it into our Slack channel. While the native Jira and Confluence skills are working perfectly, I’m having trouble with the GitHub MCP (Model Context Protocol) integration.

The Goal:
I want the Rovo Agent to be able to retrieve logs and status information from GitHub Actions pipeline links or specific repositories mentioned in Slack.

The Problem:
Even though I have enabled the GitHub MCP server and all its associated skills in the Agent configuration, every time I ask a question that requires GitHub access, Rovo responds with:

"This response was generated without using the following MCP server(s), because you're currently not authenticated. Your response quality may improve if you authenticate to these servers. Select the server(s) you'd like to authenticate to:"

What I’ve Tried:

1. Verified the GitHub MCP is enabled in the Agent's "Skills" section.

2. Ensured the Agent has the correct instructions to use GitHub tools.

3. Checked that my Atlassian account is linked, but the prompt for GitHub authentication keeps appearing.

Questions:

1. Is there a specific step to perform a "Service Principal" or "Admin-level" authentication for the GitHub MCP so the Agent doesn't require individual user auth every time?

2. Are there specific OAuth scopes or GitHub Organization settings (like third-party application restrictions) that might be blocking Rovo from maintaining a session?

3. How can I ensure the Agent uses the authenticated connection to parse pipeline links?

Any guidance on how to fix this authentication loop would be greatly appreciated!

[Dr Valeri Colon _Connect Centric_]

@Vladyslav Berezhetskyi welcome to the community. The GitHub MCP connection is separate from the GitHub for Atlassian app. For external MCP servers, Atlassian currently uses OAuth 2.1 user authentication; I don’t see a documented shared service-principal/admin login that removes per-user auth. Your org admin can approve the MCP server and tools, but users still need to authenticate to GitHub when those tools are invoked. If Slack keeps looping after successful auth, I’d treat that as an integration issue and raise it with Atlassian Support.

[Ben Spillane]

Hi @Vladyslav Berezhetskyi , 

Thanks for the detailed post, you've provided a lot of context to work off.

My first question is:

• Do you hold any Atlassian Admin roles, such as site Jira Administrator or Org Admin?

In addition to Rovo Agent configuration and skill enablement, there are a couple of other places that you'll need to ensure are configured correctly:

1. Jira site configuration of the "GitHub for Atlassian" app. This is a connector developed by Atlassian that sets up the OAuth link between your Atlassian Org. and the GitHub Org you're integrating with. This connection also provides the nomination of included repository scope. (This configuration requires the Jira Administrator role)
2. Organisation level configuration of MCPs. MCP connections are governed at the Org. level and allow for reasonable control over what connections are permitted. You will need to hold the highest level of administrative privilege to view and configure these settings.

So my advise is, if you've got the mentioned admin roles then check configurations related to (1) and (2). If you don't have these roles then consult with your Atlassian admins who'll likely be able to assist.

I hope this steers you in the right direction.

Regards,

Ben