Shopify's built-in crypto options are limited and expensive. Here's how to add USDT, Bitcoin, and other crypto payments to your Shopify store using a custom integration — without paying Shopify's 2% fee.
Shopify supports crypto payments through its payment provider integrations, but the options are limited: Coinbase Commerce and a few others that charge premium fees on top of Shopify's own transaction fees. Merchants processing high volumes pay twice — once to Shopify and once to the payment processor. There is a better way.
Shopify's Crypto Payment Options in 2026
Option 1: Shopify-Native Integrations (Coinbase Commerce, etc.)
Shopify has a small list of approved crypto payment providers in its Payment Providers settings. These integrate cleanly with Shopify's checkout, but: (1) Shopify charges an additional 0.5%–2% transaction fee on top of the processor's fee when not using Shopify Payments, (2) the available providers have limited coin support and often batch settlement.
Option 2: Custom Payment App (Recommended)
Shopify allows custom payment apps via its Payment App API (introduced in 2022). You build a lightweight payment provider that Shopify integrates with at checkout. The customer selects 'Crypto' at checkout, your app handles the payment flow, and Shopify marks the order as paid on webhook confirmation. No extra Shopify fees on this model — it's treated as an offsite payment provider.
Building a Shopify Crypto Payment App
The core integration requires: (1) a Shopify app registered in the Partner Dashboard, (2) a payment session endpoint that creates a Bekena invoice, (3) an offsite payment page showing the crypto address, (4) a webhook handler that calls Shopify's Payment Session Resolve API on confirmation.
- 1Create a Shopify Partner account and register a new public app
- 2Enable the "Payment Extension" capability in app settings
- 3Build a payment session endpoint: receives Shopify checkout data, creates Bekena invoice, returns redirect URL to your payment page
- 4Build the payment page: shows crypto address, QR code, amount due, countdown timer
- 5Set up Bekena webhook: calls Shopify's Payment Sessions Resolve API when payment confirms
- 6Test with a development store before publishing to Shopify App Store or installing privately
Alternative: Simple "Pay with Crypto" Link
If building a full Payment App is too complex, a simpler option: add a custom payment method via Shopify's 'Manual Payment Methods' and include instructions to send crypto. This doesn't automate order fulfillment but works immediately. When a customer chooses 'Pay with Crypto', they see instructions for sending USDT to a specified address — you mark the order as paid manually after verifying on the blockchain.
Reducing Shopify Transaction Fees
Shopify charges 0.5%–2% additional transaction fee on orders not processed through Shopify Payments (US stores). For crypto payments, you're always using a third-party processor. However, the custom Payment App route (Option 2) is treated differently — it can qualify as an alternative payment method with reduced or waived additional fees. Check Shopify's current policy for your region.
Automating Order Fulfillment
The full Payment App route enables complete automation: (1) customer completes crypto payment, (2) Bekena webhook fires, (3) your app calls Shopify's API to mark order paid, (4) Shopify triggers fulfillment workflow, (5) customer receives order confirmation. The total time from payment confirmation to order paid status is typically under 30 seconds.