Shopify theme lost access to GitHub repo

Online Store and Theme Development
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1

Hi team,

I have a theme connected to my organisation’s GitHub repo. Today, on the Shopify themes dashboard, the following message is shown “Shopify has lost access to this theme’s repository”. I’ve updated the permissions, but the error message still displays.

This message does not show on the other stores that I’ve connected with my organisation’s GitHub repo.

Any help would be much appreciated, thanks.

Screenshot 2025-11-17 at 09.10.11
Screenshot 2025-11-17 at 09.10.11796×252 21.6 KB

2

Have you tried disconnecting Github and reconnecting?

3

Hi Luke,

Disconnecting and reconnecting from GitHub has remove the message.

Just curious to understand why the message show on this particular store but not the other stores, would you have any insight into this?

4

Hey @Van_Duong - this is a know issue that pops up from time to time and can happen for various reasons (mainly to do with Github synchronization). Luke’s solution is the recommended fix for this, but it is something we’ve seen happen before. If you do notice it becoming a frequent issue you’re seeing feel free to let me know and we can look into it further for sure.

6

We’ve been coming across the same problem the last few months. Is there any other solutions available? Is there a clear answer to why the problem occurs? @Alan_G

7

Hey @justinb - thanks for reaching out. When you’ve seen this happen, is it usually on the same store/theme/repo, or across multiple stores?

Could you share:

  • whether the Shopify GitHub app still has access to the affected repo in GitHub
  • whether the repo is under “all repositories” or “only selected repositories”
  • whether the repo/org was renamed, transferred, or had permissions changed recently
  • what happens after clicking Update permissions
  • whether disconnecting/reconnecting or resetting to latest commit clears it
  • whether there are theme edits in Shopify Admin that haven’t been committed back to GitHub

Just want to narrow down whether this is a known GitHub access sync issue or something we should dig into further. Hope to hear from you soon!

8

Hey @Alan

It’s happened across multiple stores

We currently have the Github app authorized for all the repos in question which point to multiple stores

Yes under all repositories

Doubt the repo was renamed, transferred, or had permissions changed recently. Org stayed same.

After clicking update permissions nothing really happens. It brings us to GH where it says its already connected

Yes disconnecting + reconnecting clears it and fixes the issue

Yes depending on the shop and how much of a difference there is between production and development we sometimes have the live theme with edits that haven’t flown back to the repo so it poses a risk and involves more time when we do the manual fix