Fabric Github Integration Account Connection Problems

[VascoC28]

Hi all,

I'm running into a persistent issue with Git integration on Microsoft Fabric when using GitHub Enterprise Server (GHE), and I'm hoping someone else has encountered this.

**Environment:**
- Microsoft Fabric workspace (ws_example)
- GitHub provider: GitHub Enterprise Server (custom domain, e.g. `xyz.ghe.com`)
- Authentication: Fine-grained personal access tokens
- Workspace is successfully connected to the repo

**The problem:**
When other team members open the Source Control panel in the connected workspace, or even if I logout from my github connection account, we see "There aren't any accounts". I try to add a new account, it creates a connection but then nothing shows up. The workspace-level Git connection (repo URL, branch, folder) is visible and correct, but the per-user account authentication is broken — no accounts appear and the flow to add one doesn't complete successfully for them.

Additionally, if the workspace admin logs out of their account in the Git integration settings, the account list becomes empty and the only way to restore the connection is to fully disconnect and reconnect the workspace from the repository.

**What we've tried:**
- Having team members use "Add account" and providing their own fine-grained token
- Checking Manage Connections and Gateways for stale connections
- Disconnecting and reconnecting the workspace (works, but is disruptive)

**Questions:**
Is there a known bug with account visibility in the Source Control panel for GHE-connected workspaces?
Is there a workaround short of disconnecting and reconnecting every time?

Any help or pointers to known issues would be greatly appreciated. Happy to raise a support ticket if this is a confirmed bug.

Thanks!

[V-yubandi-msft]

Hi @VascoC28 ,

Hope everything is fine now. If you need any more information or have any questions, feel free to reach out.

Thank you.

[KevinChant]

Only the cloud-based versions of GitHub (aka GitHub.com offerings) are officially supported. So if you're using GitHub Enterprise Server this can be why you are experiencing issues:

Overview of Fabric Git integration - Microsoft Fabric | Microsoft Learn

[VascoC28]

That's what I also thought, still it works to sync and connect it to the github since it even says you need full URL for github enterprise. The only mistake is that after logouts the accounts stay created but it only appears back when you disconnect the workspace from the repo

[V-yubandi-msft]

Hi @VascoC28 ,

May I know whether your issue has been resolved, or if you still require any additional details or clarification from our side. Please let us know.

Thank you.

[V-yubandi-msft]

Hi @VascoC28 ,

If you get a chance, please review the responses shared by @Vinodh247  . They have correctly pointed out the key points, so kindly check and let us know if you need any additional details.

Thank you all for your valuable support @Vinodh247 .

Regards,

Yugandhar.

[Vinodh247]

imo, this behaviour is not expected and is very likely a current limitation or bug specific to GitHub Enterprise Server integration in Fabric rather than a configuration issue on your side. Fabric Git integration today works most reliably with GitHub.com and Azure DevOps, while GHE (custom domains + fine-grained PATs) still has gaps, especially around per-user authentication persistence. What you are seeing (account list showing empty, add account flow not persisting, and admin logout breaking the workspace link) typically indicates that the token handshake is not being stored or resolved correctly at the user session level.

practical workarounds are limited but the least disruptive ones are... use classic PATs instead of fine grained tokens (Fabric has known inconsistencies with fine-grained PAT support), ensure tokens have full repo + workflow scopes, have each user add the account from Fabric home settings (not only from Source Control panel), and avoid logging out the admin account once the workspace is connected. If stability is critical, consider temporarily switching to GitHub.com or Azure DevOps repos, where this issue does not occur.

Bottom line: do not keep reconnecting the workspace repeatedly; raise a support ticket with logs because this is almost certainly a product issue with GHE account binding in Fabric, not a user error.

[VascoC28]

Hello! Sorry for the late response, apparently its "expected behavior" (?) which doesn't make any sense. What I discovered is that if you add the full URL repository when creating the connection this happens and it doesn't matter if it is normal github or github enterprise. The expected behavior came from microsoft part after I opened a ticket as you suggested (thank you btw). 

Overall it was not fixed, they just said it is expected and should be like this which doesn't make anysense since before you logout you get this: "This workspace will still be connected to the Git repository and you can log back in whenever you want.". And it is not true, I can't log back in and it doesn't matter if it is Github or Github Enterprise. What I found is that if you have an account connected to a repo and someone create a connection you get connected automaticaly which is something that helps the problem

[VascoC28]

Hello! Sorry for the late response, apparently its "expected behavior" (?) which doesn't make any sense. What I discovered is that if you add the full URL repository when creating the connection this happens and it doesn't matter if it is normal github or github enterprise. The expected behavior came from microsoft part after I opened a ticket as you suggested (thank you btw). 

Overall it was not fixed, they just said it is expected and should be like this which doesn't make anysense since before you logout you get this: "This workspace will still be connected to the Git repository and you can log back in whenever you want.". And it is not true, I can't log back in and it doesn't matter if it is Github or Github Enterprise. What I found is that if you have an account connected to a repo and someone create a connection you get connected automaticaly which is something that helps the problem

[V-yubandi-msft]

Hi @VascoC28 ,

Thank you for sharing your findings. After consulting with Microsoft support, this behavior is currently considered expected. It impacts both GitHub.com and GitHub Enterprise Server when connecting with full repository URLs accounts disappear after logging out and you can’t sign back in, even though the UI indicates otherwise.

This is not a misconfiguration but a limitation in Fabric Git integration at this time. Workarounds are limited, for stable usage, Microsoft recommends GitHub.com or Azure DevOps until this behavior is addressed.

Thank you for being a part of the community.