Custom payment processors with Headless Shopify

Going headless with Shopify will allow you to implement a custom payment processor, yes. In order to achieve this, a custom checkout flow will need to be developed within the headless storefront that handles the transaction instead of being routed through Shopify Payments or Shopify payment gateways.

Upon transaction success, Shopify is then pinged with the full information about the order and is subsequently marked as paid programmatically. This circumvents the Shopify checkout and its payment processors, but means that you’ll need to implement a third party payment provider(s) instead, as well as any cross referencing of orders to your third party gateway when users attempt to retrieve their order history.

Shopify Plus is not required as part of this kind of setup, because the checkout / transaction is no longer routed through Shopify. After transaction success, a Shopify Order or DraftOrder query must be invoked in order to create a corresponding order in Shopify.

At Cocoon, we like to additionally append a custom property on the order to include the corresponding ID of the third party transaction, so that Shopify orders can be traced back to an individual transaction.

If offering multiple payment methods as part of a fully custom checkout (sans Shopify), an even better solution is to store a record of all individual checkouts and transactions in a custom database, which references both the payment processor, the payment processors transaction ID, and the corresponding Shopify order ID. This creates a single source of truth that can be used to relate customer purchase activity across platforms.