Stripe options disappeared at checkout after migrating to Shopify Checkout from Recharge Checkout

Shopify Apps
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Topic summary

A store owner migrated from Recharge Checkout to Shopify Checkout for subscriptions, after which Stripe card payment options vanished at checkout for subscription items only. PayPal still appears, and Stripe continues working for non-subscription purchases.

Key details:

  • The store is in Malaysia (ineligible for Shopify Payments) but should qualify to use Stripe for subscriptions according to Shopify documentation
  • Backend shows Stripe is still active
  • Both Stripe and Recharge support redirected the issue to Shopify, who hasn’t provided a solution yet

Suggested troubleshooting:

  • Check Recharge → Settings → Payment Processors to verify Stripe is listed under Shopify Checkout integration
  • Request Recharge support to reconnect Stripe as the “Shopify Checkout Processor” for subscriptions
  • Confirm with Shopify that the Stripe gateway is properly mapped to the “subscriptions_contracts” API

The issue likely stems from Stripe not being recognized as a valid subscription gateway in the new unified checkout system, despite working for one-time purchases. One respondent also suggested trying alternative checkout solutions that support Stripe for subscriptions.

Summarized with AI on October 23. AI used: claude-sonnet-4-5-20250929.
1

Hi,

I recently migrated from Recharge Checkout to Shopify Checkout for my store’s subscriptions. This was done by the Recharge team.

Stripe card options at checkout disappeared (but still shows Paypal), despite us using Stripe all this while with no problem. At the backend, Stripe is still there. It also still shows at checkout for non-subscription items.

Although I’m in Malaysia and cannot use Shopify Payments, according to this doc “eligible subscription payment processors”, we should still be eligible to use Stripe in Shopify Checkout for subscriptions.

We’ve reached out to both Stripe (telling us our account has no issues) and Recharge (who hasn’t been very helpful since the migration) and both referred us back to Shopify, who hasn’t yet been able to give us a solution.

Any idea what went wrong?

Thank you!

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2

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3

Hi there,

This issue usually happens after migrating from Recharge Checkout to Shopify Checkout for subscriptions, because Shopify Checkout requires the subscription gateway to be directly integrated through Shopify’s unified checkout system — and not through the legacy Recharge connection.

Here’s what’s likely going on :backhand_index_pointing_down:

:one: Stripe is still active for one-time purchases, but it’s not being recognized as a valid subscription gateway under your current setup. That’s why PayPal still appears, but Stripe doesn’t, for subscription orders.

:two: Recharge’s migration may not have properly reconnected your Stripe processor under the Shopify Payments API for subscription payments. Even though Malaysia doesn’t support Shopify Payments, you can still connect Stripe via the Recharge integrated method, not directly through Shopify Checkout.

:three: Solution:

  • Go to Recharge → Settings → Payment Processors and check if Stripe is listed under Shopify Checkout integration.

  • If it’s not, contact Recharge support and request them to reconnect Stripe as your “Shopify Checkout Processor” for subscription payments.

  • You can also confirm with Shopify Support if the Stripe gateway is mapped to your “subscriptions_contracts” API — that’s essential for it to appear at checkout.

Once Stripe is reauthorized through Recharge for the unified checkout, it should reappear alongside PayPal.

You can check out our Shopify Partner profile — we’ve built and shared several free Shopify app solutions to help store owners. Feel free to explore our profile and see how our apps can make your Shopify experience better!