- Short answer
- When a customer pays an invoice through Shopify Payments, you pay the card rate and no third-party fee; other gateways add a plan fee.
- Sending the invoice
- No separate invoice or link fee on any Shopify page we read, October 13, 2026
- Refunds
- Card and third-party transaction fees aren't returned
- Shopify Payments alongside a direct third-party provider
- Shopify Payments transactions carry a premium on top of standard rates
What each payment route costs
An invoice and a copied checkout link work alike: the customer pays in your online checkout. No separate invoice or link fee appears on any Shopify page we read on October 13, 2026 — the draft-order, third-party fee and pricing pages. Find your plan's card rate.
Fees by payment route on a draft order
| Payment route | Third-party fee | Processing cost |
|---|---|---|
| Invoice or link, Shopify Payments | None | Your plan's card rate |
| Card keyed in your admin | None | Higher card fees (US); no rate printed |
| Marked as paid (cash on delivery, bank deposit) | None | None from Shopify — it captures no payment |
| Invoice or link, third-party gateway | Your plan's rate | Provider's own fees |
Shopify Help Center draft-order and fee pages, read October 13, 2026.
What a third-party gateway or refund adds
On a draft order, a supported third-party card provider brings the same third-party fees as online orders: 2% on Basic, 1% on Grow, 0.6% on Advanced, 0.2% on Plus, plus the provider's own fees. See how the surcharge adds up.
Alongside such a provider, Shopify Payments transactions carry a premium of 1.25% on top of standard rates. When Shopify Payments is your primary payment provider, PayPal transactions are exempt from third-party transaction fees.
What rate does a keyed-in card get?
Shopify's US Shopify Payments rates page says manually entered card payments, which it defines as card details you enter through draft orders in the admin or through Shopify POS, are subject to higher fees. It prints no number for the admin route, and neither did the draft-order, Shopify Payments fee or pricing pages we read on October 13, 2026.
Keying in the card through Collect payment > Credit card works only with Shopify Payments, after identity verification; Shopify's draft-order payment page says you then pay only the credit card processing fees, with no third-party fee. Ask Shopify Support before keying in a large order, or see how each payment route works.
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