Why is a merchant that uninstalled our app seeing charges two months later?

Shopify App Store
1

We’ve just had a merchant reach out with this incredibly confusing experience:

We installed the app [app name] on 7 July 2025 and uninstalled it on 24 July 2025 (confirmed in our App History).

Despite uninstalling it, the app continued to generate charges on our Shopify invoices:

4 August 2025: €8.68

4 September 2025: (appears as part of ongoing billing cycle)

4 October 2025: €12.98 (currently processing)

These charges were made after the app was uninstalled and inactive, and therefore should not have been billed.

I kindly request a full refund for all charges made after 24 July 2025 and confirmation that the app’s billing has been permanently stopped.

We have simple recurring monthly subscriptions, no usages charges.

Is this merchant experiencing a bug or is this normal?

I gave the merchant the best explainer I could and also linked them the Shopify help article - which is about as much as we can do to alleviate such a poor merchant experience. I also gave them a refund for the only charge we could see on our end.

https://help.shopify.com/en/manual/your-account/manage-billing/billing-charges/types-of-charges/third-party-charges/app-charges#shopify-billing-cycle

I’ve read the article several times and honestly still don’t understand it - especially in the context of the issue above.

Suggested improvements for messaging

  • More detail on billing reports for merchants to understand why they are seeing a charge
  • The removal of pending charges for uninstalled apps until they become ‘finalised’
  • or some clearer messaging about why they are even seeing a charge for an app they uninstalled over a month ago.
  • The ability to ‘pre-authorise’ a refund to negate a pending charge that will finalise at a later date
  • The ability to remove a pending charge that will inevitably be removed at the end of the billing period
  • More transparency from Shopify to explain that all billing is actually handled by Shopify, not by app developers.
1 Like
2

Hi @Anthony_SL,

I can confirm that app billing should automatically be cancelled as soon as the app is uninstalled from the store, or paused when the store is frozen, as described in our Shopify.dev documentation.

When an app is uninstalled, Shopify automatically cancels the subscription. A credit isn’t applied to cover the cost of the rest of the billing period. Merchants can reinstall and use the app for the remainder of the billing period.

When a store’s billing account freezes, associated app subscriptions also freeze.

If the merchant is seeing otherwise, and the app was confirmed to be uninstalled, I would recommend advising the merchant to reach out to Shopify Support directly, via the Shopify Help Center and we can help look into this in further detail.

You can reach out via the Shopify Help Center as well, though it would be best if the merchant could reach out while logged into a staff account connected to the store in question, so we have the full authentication to review the invoices on the merchants store internally to aid our investigation.

3

Thanks @Kellan-Shopify - I’ve asked the merchant for more info and will pass on to reach out to Shopify support.

Have you got a direct link for them to be able to lodge a ticket and/or bypass the AI bot?

4

At this time there is no direct links to get a live human chat, they will have to reach out through the AI bot first, as it will help gather context from the merchant to ensure our support advisors have enough information on our end to be able to help them as quickly and efficiently as possible.

5

Thanks Kellan. Appreciate it. I’ll confirm the additional information from the merchant first and then get them to reach out.

As a side note - I’d love if some of the feedback could be logged as feature requests/suggestion.

Particularly this one:

  • The ability to ‘pre-authorise’ a refund to negate a pending charge that will finalise at a later date.

It’s a horrible experience to tell the merchant we can’t process the refund until it appears on our end sometime in the future.

6

Hey @Anthony_SL,

I’m happy to help send some feedback on your behalf on pre-authorizing refunds. To help us ensure we have the full context for the feedback, can you provide some additional information on the request. Specifically the following.

  • In what use cases do you find this limitation is occurring, where you need to tell a merchant you can’t process a refund until it appears on your end?
    • Is this for refunds after a merchant uninstalls the app, or some other workflow/use case?
    • If this is for refunds after an uninstall, it might be that the charge hasn’t even been paid or invoiced to the merchant yet, since app billing cycles don’t always line up with merchant billing cycles, as discussed in the Help Center here.
  • Is there any current documentation you are following for this, for reference.
  • Is there any current workarounds you are using in the meantime?
7

Hi @Kellan-Shopify

It’s for this exact use case:

If this is for refunds after an uninstall, it might be that the charge hasn’t even been paid or invoiced to the merchant yet, since app billing cycles don’t always line up with merchant billing cycles, as discussed in the Help Center here.

The process is effectively:

  • Merchant is billed automatically after the trial ends
  • Merchant uninstalls a few days later
  • Merchant sees a charge for the app on their upcoming bill and reaches out for a refund
  • We don’t see an option to refund the charge when viewing it in Partners dashboard
  • We can’t process a refund for the customer until their bill is finalised (which could be weeks later).

Workarounds in the meantime is just to set a reminder to check the charges in Partners every week to see if it’s been finalised and if we can refund the merchant.

I haven’t tested with providing an ‘app credit’ to negate the cost, but this doesn’t really solve the underlying issue.

Thanks!

8

Hey @Anthony_SL,

Thanks for that context, I will be submitting this as feedback internally!

I can confirm for now though that this is a known limitation, and is documented in the Shopify.dev docs, and does actually recommend to use App Credits in these situations.

  • You can only refund charges that the merchant has paid for. If an app charge hasn’t been paid, then you can credit the charge to remove it from the merchant’s bill.
1 Like
9

I definitely missed that note because I was searching in the merchant facing help docs to try to understand what the merchant should see/request. :man_facepalming:

Good to know! Thanks.

1 Like