Short answer: no. When you refund an order paid through Shopify Payments, Shopify does not give back the card processing fee it charged on the original sale. It also does not charge you a new fee for making the refund. So a refund costs you the fee from the sale, and that is how it is meant to work.
Full refunds and partial refunds
Shopify’s Help Center says that when you process a refund, “no additional transaction fee is incurred”, and that “the original credit card transaction fee isn’t refunded to you when issuing a refund”. On the page about refunding orders it adds that if the order was processed through Shopify Payments, you don’t get any credit card fees refunded. Shopify also says this holds whether or not the order was fulfilled, so cancelling an order before it ships does not bring the fee back either.
Shopify’s pages don’t give a separate rule for partial refunds. They describe one rule for all refunds: the original fee is not returned. If you want to be sure for your own store, ask Shopify support.
The refund itself comes out of your next available payout, not the one that held the original sale.
Two different fees
Sellers often mix up two charges, and they are not the same thing.
The card processing fee
This is what Shopify Payments charges on each card transaction. The rate depends on your plan. It is taken out of the sale before the money reaches your payout, and it is the fee in the Fee column of the export. On a refund, it is not returned.
Shopify’s third-party transaction fee
This is a separate fee for using a payment provider other than Shopify Payments. Shopify says that if you use Shopify Payments as your sole payment provider, there are no third-party transaction fees on orders. If you do take payments through another provider, the Help Center says “third-party transaction fees aren’t returned to you when you issue an order refund”. Shopify’s page on refunding orders also describes some gateway-specific cases, so if this is you, read it for your own situation.
In short: with Shopify Payments you will see a card processing fee and no third-party fee, and neither comes back on a refund.
Where you can see it in the export
In the payout transactions export, each row has a Type (for example charge or refund), an Order number, an Amount, a Fee and a Net, which Shopify defines as the difference between the amount and the fee. A refund shows up as its own row, with its own Type, separate from the sale it belongs to.
Example only. The order numbers and amounts below are made up, in US dollars, to show the pattern. They are not from a real store.
| Type | Order | Amount | Fee | Net |
|---|---|---|---|---|
| charge | #1001 | 100.00 | 3.20 | 96.80 |
| refund | #1001 | -100.00 | 0.00 | -100.00 |
| charge | #1002 | 50.00 | 1.75 | 48.25 |
| refund | #1002 | -20.00 | 0.00 | -20.00 |
This is an example. Your own export may show the refund row slightly differently.
Order #1001 was sold for $100.00 with a $3.20 fee, so $96.80 reached your balance. It was then fully refunded: $100.00 went back to the customer, no new fee was charged, and the original $3.20 was not returned. Across the two rows you are down $3.20, which is the fee. Order #1002 was a partial refund of $20.00 on a $50.00 sale, and the $1.75 fee on the sale stays as it was.
Why a kept fee is normal
Shopify’s own explanation is that credit card fees aren’t refunded on Shopify Payments transactions because Shopify Payments incurs costs to process both the refund and the original transaction. A fee that stays after a refund is therefore documented policy, not a missing credit and not a mistake, and there is nothing to claim back. It is worth knowing about if you refund often, because it is a real cost.
When it is worth a look
These are different from a kept fee, and each is worth checking:
- A fee charged twice on the same sale, with two charge rows for one order and nothing to explain it.
- A fee on a refund row. Shopify says refunding incurs no additional transaction fee, so a new fee there is a question for support.
- A refund larger than the sale it refers to, such as the same order refunded twice.
- A refund with no matching sale. This is often harmless, because the sale may be in an earlier payout, so look for it there before worrying.
How PayoutCheck shows it
PayoutCheck lists the processing fees Shopify kept on refunded orders under “Processing fees on refunded orders”, with the total, shown for your information. It is not counted as a discrepancy, because it is standard Shopify policy. The things in the section above are the ones it checks for and reports.
Questions
Does Shopify refund the processing fee when I refund an order?
No. Shopify states that the original credit card transaction fee isn't refunded to you when issuing a refund. The customer gets their money back, and the fee you paid on the original sale stays with Shopify.
Does Shopify charge a fee to process a refund?
No. Shopify states that when processing a refund, no additional transaction fee is incurred. The only cost is the original fee, which is not returned.
Is a partial refund different?
Shopify's pages don't give a separate rule for partial refunds. They describe one rule for all refunds: the original fee is not returned.
What is the difference between the processing fee and the third-party transaction fee?
The processing fee is what Shopify Payments charges on each card transaction. The third-party transaction fee applies only when you use a payment provider other than Shopify Payments; Shopify says there are no such fees if Shopify Payments is your sole provider. Shopify says third-party transaction fees aren't returned when you issue an order refund.
Is a fee that was not returned a mistake I should dispute?
No, it is Shopify's documented policy. It is worth a look only if a fee was charged twice on one sale, a refund row carries a new fee, a refund is larger than its sale, or a refund has no matching sale in any of your payouts.
Sources
- Shopify Payments refunds: help.shopify.com
- Creating returns and refunds: help.shopify.com
- Third-party transaction fees: help.shopify.com
- Cost of Shopify Payments: help.shopify.com
- Viewing and exporting your Shopify Payments payout details: help.shopify.com
This guide describes Shopify’s own published documentation as of 1 October 2026, which can change. It is not accounting, tax or legal advice, and PayoutCheck is not affiliated with Shopify.