GitHub pull requests not showing in Jira? How to find and recover them

First: open the issue itself

Before anything else, open the Jira issue and look at its Development panel. Don't rely on a filter, a board or a JQL search such as development[pullrequests].all = 0.

In our own tests, Jira's search and the issue's Development summary lagged behind the panel. After a burst of pull requests, about a third of the issues still showed no PRs in search hours later, although the PRs had arrived. Opening an issue brought its search result up to date within a minute or two; issues nobody opened stayed out of date for days. So a search can tell you a PR is missing when it isn't.

You'll need Jira's View development tools permission to see the panel. Without it, every issue looks as if it has no development work.

Is it lost, or just slow?

New pull requests normally appear on their issue within minutes. In our tests most arrived within about half an hour, and the slowest took about seven and a half hours.

So a PR that still isn't on its issue a day later isn't slow. Something stopped it, and in our experience nothing will bring it in on its own.

Step 1: check the key

GitHub for Atlassian links a pull request to an issue by the issue key (for example KAN-123). Atlassian's guidance is to put the key in the pull request's title, and in the branch name and commit messages, written in capitals. Its backfill also looks for keys in the PR's description and source branch.

• Check the key is spelled exactly, in capitals, and belongs to a project on this Jira site.
• If the project was renamed or the issue moved, the PR may carry the old key.

Step 2: check the connection

• In Jira, go to Apps → Manage apps → GitHub for Atlassian, and check your GitHub organization is listed.
• If the organization was connected with Only select repositories, new repositories aren't added automatically. Check the PR's repository is included in the app's repository access on GitHub.
• Look at other PRs from the same repository around the same time. If they're in Jira and this one isn't, the connection is working and this PR was dropped. If none are, the repository probably isn't connected.

Step 3: check what was happening when it was opened

The tricky part is that a PR can be lost while everything still looks connected. On 21 October 2026, during a GitHub incident that delayed webhook deliveries, we opened a pull request in a test repository. Its branch and commit reached Jira; the pull request never did. PRs opened hours before and after arrived within minutes. Nothing showed an error, and nothing resent it afterwards.

So if a PR is missing, check GitHub's status history for incidents affecting pull requests or webhooks around the time it was opened. Other PRs from the same window may be missing too.

Step 4: bring it back

For one or two PRs: edit them. Change the pull request's title (adding and then removing a character is enough) or push a commit to its branch. GitHub then sends the PR to Jira again. In our test, a missing PR appeared on its issue straight after an edit.

For many PRs, or a whole period: run a backfill. This needs a Jira admin.

• In Jira, go to Apps → Manage apps → GitHub for Atlassian.
• Open the settings for your GitHub organization and choose Continue backfill.
• Pick a start date before the oldest missing PR, then Backfill data.
• Afterwards, open a few of the affected issues to confirm their PRs arrived. Don't trust a search for this (see above), and don't take "finished" as proof: Atlassian's public issue tracker has a report of a backfill finishing without importing anything.

Why nobody told you

GitHub for Atlassian shows whether an organization is connected, not whether every pull request arrived. When an event is lost, nothing tells you. Customers have asked Atlassian for exactly this: a notification when syncs fail, because "failed repository syncs can go unnoticed".

It matters most where Jira is the record of what changed: release notes, change approvals, and audits that expect every code change to trace back to a ticket.

Finding them across a whole site

Checking by hand means listing recent pull requests that carry issue keys, asking Jira which of those issues show none, and then opening each one to rule out a stale search. That's slow for a busy team.

So we built Pull Request Watch, a Jira app that does it for you. It compares your GitHub pull requests with Jira's development data, checks every suspect twice and again with Atlassian's Teamwork Graph, and lists only the issues where Jira shows none of their pull requests. It reads pull request details only, never your code. It's in private testing: if you'd like to run the free audit on your site, email support@quietpenguin.com.

GitHub and Jira are trademarks of their owners. Quiet Penguin is independent and isn't affiliated with or endorsed by GitHub or Atlassian. GitHub for Atlassian is moving to a new platform in late 2026, so its screens and names can change; if something here doesn't match what you see, tell us and we'll update it.