GitHub for Jira App: Commits/PRs not syncing and Backfill pulls 0 data after disconnect

[Tej sharma]

I am experiencing an issue with the official GitHub for Jira integration where development data has completely stopped syncing to the Jira issue Development panel, and the backfill function is no longer pulling in data.

The Context:

• Environment: Jira Software Cloud
• Integration: Official GitHub for Jira App installed via Atlassian Marketplace
• Format: I am strictly following the naming conventions. My branch name (feature/KAN-1-practice), commit messages (KAN-1: practice integration run), and PR titles all contain the exact Jira issue key.

How the issue started: Initially, the integration worked. It successfully synced my very first pull request and displayed it correctly under the KAN-1 ticket. However, any subsequent commits or new pull requests I made using the exact same KAN-1 key failed to appear in Jira.

Troubleshooting Steps I have taken: To attempt a fix, I completely disconnected the GitHub Organization from within the Jira Apps configuration page and then freshly reconnected it.

Since doing this, things have gotten worse:

1. Because of the disconnect, the historical data for the first (working) PR was understandably wiped from the Jira issue.
2. I triggered a Continue backfill. The status quickly changes to FINISHED, but it pulls in 0 data. My old PR did not return, and none of the new PRs or commits are showing up.
3. On the GitHub side, I have verified the GitHub App configuration (Organization Settings -> GitHub Apps -> Jira -> Configure) and ensured that Repository access is correctly pointing to the required repositories / set to All repositories.

It seems like the webhook or authorization link between GitHub and Jira is permanently severed for this project, even though the Jira UI says Connected and Backfill Finished.

Has anyone run into this problem before or know how to force Jira to properly recognize the GitHub repository again? Any help would be greatly appreciated!

[Benjamin]

Hi  ,

I have done several of these integration for cloud instances and I haven't heard of anything reported like this. It has been a set it and forget it situation. My usual first thought is to reset the integration which you have done...so, that's a good start.

The next step is to check if Github has logs that you can review to see if what connection or errors pop up. I might provide some indication wether its a API, authentication, or a connection issue. The 2nd thing to do with to raise a ticket with Atlassian support since you are on paid plan.

Thanks,

Ben

[Carlos Garcia Navarro]

Hi @Tej sharma ,

In GitHub → Org Settings → GitHub Apps → Jira → Configure, try to switch from “All repositories” → “Only select repositories”. Save, and then switch back to “All repositories”.
This may enforce a refresh of permissions.

If that doesn't work, can you reinstall it?

[Arkadiusz Wroblewski]

Hello @Tej sharma 

Isn't it similar to your Problem?

https://jira.atlassian.com/browse/JRACLOUD-91945