Webhooks Automatically Disappearing After Deploying Shopify App

Hello Shopify Community,

I’m encountering an issue with webhooks in my Shopify app. After deploying the app using Shopify CLI, the webhooks configured in the shopify.app.toml file work fine initially but disappear after some time. Specifically, the following webhooks are affected:

  • app/uninstalled
  • shop/update
  • orders/paid

The GDPR webhooks (customers/data_request, customers/redact, shop/redact) remain intact. Here’s the relevant configuration in my shopify.app.toml:

[webhooks]
api_version = “2025-04”

[[webhooks.subscriptions]]
topics = [ “app/uninstalled” ]
uri = “url/hooks/app/uninstalled”

[[webhooks.subscriptions]]
topics = [ “shop/update” ]
uri = “url/hooks/app/updated”

[[webhooks.subscriptions]]
topics = [ “orders/paid” ]
uri = “url/hooks/order/paid”

Issue Details:

  • I’m using Shopify CLI to deploy with include_config_on_deploy = true.
  • The webhook endpoints use HTTPS and are set up to return a 200 OK status.
  • I’ve checked and found no email notifications from Shopify about webhook failures or deletions (including spam/junk folders).
  • The app has the necessary scopes (read_orders, etc.) and hasn’t been uninstalled during testing.

Questions:

  1. Has anyone experienced similar issues with webhooks disappearing automatically? What could be the cause?
  2. Is there anything wrong with my shopify.app.toml configuration or Shopify CLI deployment process? How can I ensure webhooks are registered and persist reliably?
  3. Is there a way to check the specific reason why webhooks are being deleted (e.g., via Partner Dashboard or API)?

Any suggestions or insights would be greatly appreciated! Thank you, community.

Do you know how long some time is? :thinking:
Are we talking minutes or days for example.

Is anyone else working on the application?

In your Shopify Partner Dashboard can you see any information under Performance > Webhooks?

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