B2B Checkout - Payment method is saved to company instead of customer, breaking Recharge compatibility

We’re implementing subscriptions for B2B customers using Checkout UI Extensions, since Shopify doesn’t currently support native subscription flows for B2B accounts.

During testing, we found that when a B2B customer adds a payment method for the first time at checkout, it gets saved at the company location level, not directly on the customer record.

This becomes a problem because Recharge requires the payment method to be assigned to the customer, not the company, in order to process subscription billing.

Shopify support confirmed this is a current limitation, but we’d like to know:

  • Is there any workaround or undocumented way to programmatically associate the payment method with the customer during checkout?
  • Is this on the roadmap to be addressed for B2B use cases?
  • Are there any recommended patterns or alternatives for enabling subscriptions for B2B customers that maintain compatibility with Recharge?

We’ve also contacted Recharge, but are opening this here to explore potential paths on the Shopify side.

Thanks in advance to anyone who’s worked with this and can offer guidance.