App register both to shop specific and config managed webhooks

Hi everyone,

I’m running into an issue with my Shopify app where I see duplicate webhook subscriptions for the same topic and address, even after I’ve deleted all shop-specific webhooks using the GraphQL Admin API.

What I’ve tried:

  • I use the webhookSubscriptionDelete mutation to remove all webhooks for a shop.

  • I verify that the webhooks are deleted (querying returns none).

I found that on every app install the shop-specific webhooks are being registered. but where this things happen? (I don’t see them in my code)

Extra context:

  • My stack is: MERN by Shopify express template.
  • libraries used: @shopify/shopify-app-express@latest
  • I’m using the 2025-01 Shopify API version.

I want to use only the config managed webhooks.
Has anyone else experienced this?

Thanks in advance for any insights!