Short answer: No. When you issue a refund in Shopify, shipping charges aren't included by default — only the item amount is refunded. To refund shipping too, you have to add it manually during the refund.

This applies to every Amazon-synced order in your Shopify store, regardless of how it was created.

How to refund shipping along with items

1. Open the order in Shopify and start a refund.
2. Enter the shipping amount you want to refund in the Refund shipping field.
3. Click Refund.

If you leave Refund shipping empty, only the item amount is refunded — shipping stays with you.