How to consolidate GitHub issues into a single Jira Cloud project?

[Zoya Khan]

What’s the best way to integrate and consolidate issue data from multiple GitHub repositories into a single Jira project for centralized tracking and reporting?

I’m looking for a reliable solution to automatically sync GitHub issues (including fields like title, description, status, labels, and assignees) from multiple repos into one Jira project. Ideally, I want to maintain two-way sync so that updates in Jira reflect back in GitHub.

Has anyone implemented this using native integrations, webhooks, or a third-party app (like Exalate or similar)? I’d also appreciate any best practices for field mapping, handling status transitions, and avoiding data duplication.

Environment: Jira Cloud + multiple GitHub repos.

Any architecture suggestions, automation workflows, or examples would be great.

[Aron Gombas _Midori_]

Surprisingly, there are multiple apps that provide bi-directional syncing between GitHub and Jira Cloud. They sync not only work items, but other entities as well.

I think you should run your own research. Implementing this with webhooks and APIs can be quite an effort, so I'd try to find a ready-made app instead.

[Diana_Architect_ZigiWave]

If you want to bring issues from multiple GitHub repositories into a single Jira Cloud project, there are a few approaches you can take depending on how much automation and two-way sync you need.

1. Native GitHub + Jira integration (basic, but limited)
The built-in integration works well for development visibility, but it doesn’t support full issue synchronization or consolidating issues from multiple repos into a single Jira project. It’s mostly one-way and doesn’t let you control field mapping or statuses. If you need full sync, you’ll likely outgrow this quickly.

2. Custom automation using GitHub webhooks + Jira Automation
This gives you flexibility, but requires engineering time. Typical setup:

• Use GitHub webhooks to POST issue events into Jira.

• Jira Automation rules create/update issues based on the payload.

• Webhooks back to GitHub update labels, assignees, or status.

This can work, but becomes complex when you need:

• Two-way sync

• Status/state mapping

• Bulk updates

• Avoiding loops or duplicates

• Consistent mapping across many repos

You need a clear data model and governance to keep it maintainable.

3. Third-party integration apps (most practical for full sync)
If you want all GitHub issues from multiple repos to appear in one Jira project with reliable two-way sync, an app is usually the most sustainable. They typically give you:

• Automatic issue creation and updates

• Field mapping (title, description, labels, assignees, etc.)

• Status mapping/workflow transitions

• Controls to choose which repos sync to which Jira projects

• Deduplication logic

This ends up being easier to manage, especially as the number of repos grows.

Best practices regardless of method

• Define a unified workflow for the consolidated Jira project.

• Map GitHub labels → Jira fields consistently.

• Decide which system is the source of truth for each field.

• Use prefixing if multiple repos have overlapping issue numbers.

• Avoid syncing internal/automation labels unless necessary.

Light note: If you do explore integration apps, tools like ZigiOps (check it out on the Atlassian marketplace)  can also handle this type of multi-repo → single-project issue sync with customizable field and status mappings — just as an option. You can give it a try & book a demo with our team or start your free trial. 

[Javier Pozuelo -Exalate-]

Hi @Zoya KhanI’m the Community Manager at Exalate.

You can definitely "consolidate" issues from multiple GitHub repos into a single Jira Cloud project. The native GitHub - Jira integration is good for branches, commits, PRs, etc. If you want full issue synchronization, including fields, labels, assignees, comments, and status transitions, you’ll need either custom webhooks or a third-party connector.

As you mentioned, tools like Exalate are built for this setup. You can sync many GitHub repositories into one Jira project, control field mapping with scripts, handle status transitions cleanly, and avoid duplication by defining your own matching rules. Each repo can push to the same Jira project while keeping updates flowing both ways.

As for the best practices, for field mapping and statuses, the safest approach is to map only the fields you actually need on both sides. For data duplication, as long as you have correct mappings, correct configuration, and you don't have duplicated triggers, you shouldn't come across data being duplicated.

You can reach out to us in the Exalate community in case you have any questions.

Good luck with your implementation!