Auto-deploy breaks when multiple private GitHub repos are linked - must unlink/relink every time

Support
1

Hey Netlify community,

I’m running into a frustrating issue with auto-deploys and would love some help or insight.

Here’s what’s going on:

  • I have private GitHub repositories, each linked to its own Netlify site.

  • During the setup, I haven’t given Netlify access to all my GitHub projects - just the ones I want.

  • The issue: when auto-deploy works on one site, it causes the other site to fail.
    I then have to manually unlink and relink the broken one from GitHub for it to deploy again. This cycle repeats - fixing one seems to break the other!

  • I confirmed that my deploy settings are correct, and the builds work fine once the link is refreshed - so it’s not a build error or code issue.

Is this a known limitation with Netlify + private repos + selective GitHub access?
Or is there a permanent fix I’m missing so I don’t have to keep relinking every time I push changes?

Would appreciate any guidance!

Thanks in advance!

2

Me again. I think I may have fixed it.

I went to GitHub > Settings > Applications

This was my setup:

github-select-repos
github-select-repos885×219 15.2 KB

I changed the access to ALL REPOSITORIES & confirmed the change.

Back on Netlify, I triggered a deploy, and it worked! It didn’t fail like previously, and I didn’t have to Unlink-Link.

The issue sounds like a problem with how Netlify manages OAuth permissions for GitHub on per-site basis when repos are private and access is restricted to only selected ones. So, that means when you initially authorize GitHub access, you’re either giving access to all repos or only selected repos. If you chose selected repos, each time you “Link” a new site, you’re basically refreshing that permission scope. This means you are overwriting access every time you relink one project.

Hope I am making sense. I will monitor and come back with any updates.

6

Hey @manojk :wave:,
Thanks for reaching out!

We’ve gone ahead and created a support ticket for you, so our team can follow up with you directly via email from the help desk. Our Support crew will be in touch with you by email soon.

Great news: these days anyone can reach out to Netlify Support. First, you can try getting an answer using Ask Netlify, our helpful AI search tool. If your question isn’t answered there, you can submit a ticket using the support form, and we’ll take it from there.

We’re keeping the community around for swapping ideas, sharing tips and tricks, and talking shop with other folks building on the platform — but for support issues, tickets are the way to go.

Thanks for being here, and keep an eye out for that email from us!