Yes Shopify accepts Apple Pay for subscriptions on their platform.

The payment methods that a Shopify store accepts depends on each store.

The store would actually need to have Apple Pay set up as payment method under Shopify ➡ Settings ➡ Payments

For more information about setting up your Payment Settings in your Shopify store, please contact Shopify Support directly.

Ongoing™️ works with Apple Pay for Shopify Subscriptions.

Feel free to use Ongoing Subscriptions with your Shopify store, & Apple Pay.