Issue with Payment Method Update Page Loading Old checkout.liquid contents

Shopify Plus
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Topic summary

Persistent bug: the payment method update page continues to inject legacy checkout.liquid content (e.g., PayPal and custom JavaScript) even after full migration to Checkout Extensibility and deletion of checkout.liquid, causing script conflicts.

Scope and reproduction: Affects stores that migrated from legacy checkout; stores created directly in the post–Checkout Extensibility era do not show the issue. Shopify Admin indicates no existing checkout.liquid, yet the behavior persists.

Suspected cause: Backend caching or references on Shopify’s servers tied to the payment update confirmation endpoint (/payment_methods/confirm?key=…), which is typically reached via the Admin GraphQL mutation to send the payment method update email.

Attempts and support: Extensive troubleshooting (theme/config resets, code comparisons, screen recordings) has not resolved it. Multiple merchants report that Shopify support attributes it to customizations but they cannot edit checkout.liquid since it no longer exists.

Workaround noted: An Admin link to a checkout customizations report page (replace [storename] in the URL) can disable scripts, but cannot remove legacy customizations.

Status: Unresolved and ongoing; merchants request escalation to Shopify engineering and seek community insights.

Summarized with AI on November 25. AI used: gpt-5.
1

Hi Community,

I’m reaching out to discuss a persistent issue we’ve encountered related to the payment method update page on our Shopify stores. We’ve fully migrated to Checkout Extensibility, but we are experiencing problems where contents from our old (and already deleted) checkout.liquid file are still being injected on the payment method update page. Here’s a detailed breakdown of our situation:

Background:- Migration to Checkout Extensibility: We migrated to Checkout Extensibility, and since then, our checkout process has been functioning correctly without loading any contents from thecheckout.liquid. However, the payment method update page continues to reference and load stuff from this old and already deleted checkout.liquid. This leads now to some Javascript conflicts in our case.

Issue Details:1. Old Contents and Custom Script Tags Loading: Despite deleting the checkout.liquid file and re-uploading our theme (without any checkout.liquid ) the payment update page still attempts to load scripts related to PayPal and other custom JavaScript that we had previously implemented.

  1. No Third-Party References: We have very few apps installed and do not have any that would reference the old checkout.liquid.
  2. Replication of Issue: We can consistently replicate the issue across our store. The problem is exclusive to those stores that underwent the migration process; our newest store does not experience this issue, as it was built directly on Checkout Extensibility.
  3. Most strange thing: Even the Shopify admin area itself says that it can find customizations in a not existing checkout.liquid.

Attempts to Resolve:- We have engaged with Shopify support multiple times, providing detailed information, including screen recordings and source code comparisons.

  • Despite extensive troubleshooting—including resetting themes and configurations—there has been no resolution.
  • We believe the issue lies with internal caching, references and backend page creation by the shopify server that are not being updated after migration.

Request:

We would greatly appreciate any insights or advice from the community, especially if anyone has experienced similar issues or has suggestions for troubleshooting. If so please also contact Shopify support to escalate this to the backend engineering team for further investigation.

Cheers

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2 Likes
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This really is a problem. The problem does not exist on stores created in a “post-checkout-extensebility” world. It’s pretty obvious to me that there is something wrong with how the probably lesser used page https://STORENAME/payment_methods/confirm?key=SOME_KEY has been migrated by the Shopify team. To me it appears that this page is doing something unexpected on Shopify side. Anybody else had that problem?

For reference the page can be generated by sending an email via this mutation

3

We are also a Plus merchant who had checkout customizations prior to extensibility.

1 year later this is STILL affecting our store and Shopify support has been no help. We are being told fix this on our own (as it’s due to customizations) but we don’t have the ability to edit the file with customizations (checkout.liquid). Support doesn’t seem to understand this or have training around this issue.

Note: To anyone else struggling with this, replace [storename] in the link below with the correct name of your store to see checkout.liquid scripts and customizations. This is the old checkout extensibility upgrade guide. The link still exists but it is not displayed in admin settings.

https://admin.shopify.com/store/[storename]/settings/checkout/customizations-report

Note that you can disable scripts but you cannot remove customizations. Clicking the link to go to checkout.liquid opens theme code editor but of course no file is displayed as checkout.liquid is not present anymore.

@fabos @cschober360 any luck in solving this?