Handling refunds for Apple Pay transactions on Shopify is straightforward. When you initiate a refund through your Shopify admin, your customer will receive a notification about it. Keep in mind that the refund will be marked as pending for about 3-5 business days. This is the time it usually takes for the funds to return to the customer’s account. During this period, it’s good practice to inform your customers about the pending status and when they can expect the funds to appear.