How to access EMU organization repositories using custom OAuth app credentials with the remote GitHub MCP server?

[olaservo]

I'm trying to use the remote GitHub MCP server (https://api.githubcopilot.com/mcp/) with a custom OAuth app in Claude Desktop, following guidance from Anthropic support that this should be possible for servers that don't support Dynamic Client Registration.

Setup:

• Using Claude Desktop with custom OAuth app (client ID + secret)
• OAuth app is approved at organization level
• Token has repo and read:org scopes
• Organization shows as authorized
• GitHub Enterprise with Managed Users (EMU)

Current behavior:

• Can successfully access personal private repositories
• Cannot see any organizations or organization repositories
• When asking Claude to list organizations or teams, it returns none

Question: Is there additional configuration needed for the remote MCP server to properly access organization repositories when using custom OAuth app credentials? Or does the remote server only support organization access through its built-in OAuth flow or PAT authentication?

The OAuth flow completes successfully with all requested scopes granted, but the MCP server appears unable to access organization data despite the token having the necessary permissions.

Screenshot of Oauth App permissions in the EMU org I want to interact with:

Screenshot of approved Oauth App in the same EMU org:

Thanks!

[olaservo]

Posting a new comment since I had to delete my other one - for my previous comment, I hadn't noticed that I was going between 2 different orgs in relation to where the custom Oauth app was installed, vs the org repos I was trying to access through the server.

It looks like one issue with listing repos may be because there isn't a 'list repos' tool that will support this scenario. If I use the search repos tool and specify the org name, then I can see all the repos listed.

Now I have see other access errors, but those seem more related to where the custom Oauth app is actually installed or configured and not the server itself. Will post here with any more findings on how the server is trying to access these resources.