Connection of Jira security to GitHub for some project

[Pavel Backovsky]

Hello, 

We have a problem finishing setting the connection between Jira security and GitHub. 
For some projects, it is set correctly (set some long time ago), and I can see vulnerabilities and create a Jira ticket for them. 
For others, it will show the page below. When clicking on "Finish setup", a page with the settings for connecting to GitHub is displayed, which is working (second picture). 

Any suggestions where it could be a problem?
Thank you

[Javier Pozuelo -Exalate-]

 Hi @Pavel Backovsky, I’m the Community Manager at Exalate.

It sounds like the GitHub–Jira integration is partially configured—working for some projects but not others. This usually happens when:

• The GitHub organization or repository wasn’t fully authorized for security integration in the GitHub for Jira app
• The affected repositories haven’t had Advanced Security enabled on the GitHub side
• Or, the Jira integration was configured on a per-repo basis instead of at the org level

You might want to check:

• That all relevant GitHub repos have GitHub Advanced Security enabled
• That the Jira GitHub app is correctly authorized for all intended repositories/orgs
• And that the GitHub integration settings under “Security” in Jira are applied consistently across projects

I also wanted to mention an alternative approach in case you're exploring other options down the line.

There are a few more Marketplace apps that support GitHub–Jira integration 

Each solution offers different strengths—some are more focused on unidirectional integrations, while others (like Exalate) offer more advanced integrations options (e.g., across multiple GitHub instances, or syncing issues, pull requests, comments, etc.)

You might want to explore a couple of these to see which aligns best with your setup. Happy to share more context or answer any questions if you'd like to dig deeper into any of them.

Hope this helps!