Shopify Payments vs Third-Party Gateways

Shopify lets you take cards with its own Shopify Payments or with an outside gateway. The choice changes what you pay Shopify, not only the gateway. This guide uses Shopify’s help center (read 2026-10-16) and the US rates on Shopify’s pricing page, read from a US connection on 2026-10-16. Shopify shows different prices in different countries, and so confirm the rates for your market on Shopify’s site. This is general information, not financial advice.

The extra fee: third-party transaction fees

Shopify’s overview says third-party transaction fees cover the cost for Shopify to provide a secure checkout platform and integrate with external payment providers. They vary by plan and are charged when you use a third-party payment provider to accept customer payments. On the US pricing page the fees are:

The third-party fee is paid to Shopify in addition to whatever your gateway charges. Shopify’s help center says that when you activate Shopify Payments you stop paying these fees, and that if you switch from Shopify Payments to another processor you begin paying them.

When the fee does not apply

Shopify says you are not charged third-party transaction fees for orders processed with Shopify Payments, Shop Pay, Shop Pay Installments, or manual payment methods such as cash, cash on delivery and bank transfers. It also says that if you elect Shopify Payments as your primary payment provider, PayPal transactions are exempt. The exception it flags is store credit and gift cards on stores created on or after May 12, 2025: orders paid partly that way are charged third-party fees on the amount paid with store credit or gift cards.

A worked example: a $50 online order on the Basic plan

Using Stripe’s published online rate of 2.9% + 30¢ (read 2026-10-16) as the outside gateway:

• Stripe through Shopify, Basic plan: $1.45 + $0.30 = $1.75 to Stripe, plus 2% of $50 = $1.00 to Shopify, so $2.75 in total, 5.5% of the order.
• Shopify Payments, Basic plan: 2.9% + 30¢ = $1.75, with no third-party fee, 3.5% of the order.

That is arithmetic from published rates, not a quote. Your gateway’s rate may differ, and Shopify Payments may charge more for premium cards, international cards or manually keyed sales. See Shopify fees explained for those rates. A higher Shopify plan lowers the third-party fee but costs more per month; the break-even depends on your sales through the outside gateway.

Using both at once

Shopify says you can use Shopify Payments alongside one direct third-party provider in the same store. The third-party provider remains primary for credit and debit cards, with Shopify Payments as a backup that can recover failed card transactions and as the provider for methods the outside gateway does not support (Shop Pay, local payment methods). Pricing in that setup:

• The third-party provider’s card transactions are subject to third-party transaction fees.
• Transactions processed by Shopify Payments, such as Shop Pay and local methods, are charged at standard Shopify Payments rates plus a 1.25% premium.
• A failed transaction recovered through Shopify Payments is charged the standard Shopify Payments rate plus the 1.25% premium.

Shopify lists other conditions: the store must be in a country where Shopify Payments is supported, Shopify Plus merchants with signed contracts, including new and renewing, are not eligible at this time, recurring subscription charges are processed through the third-party provider by default and are not retried through Shopify Payments, and Shopify Capital eligibility is based on total sales from both providers.

How to decide

1. Check whether Shopify Payments is available in your country and for your business type.
2. Add up what each route costs on your typical order, as in the example above, including the third-party fee.
3. Look at non-fee reasons you might keep an outside gateway, such as existing contracts or payment methods. We do not assess those.
4. Re-run the numbers if your sales mix changes; use our processing fee calculator for published gateway rates.

For the wider question of whether the platform fits, see Is Shopify worth it?.

What we did not verify

We did not verify Shopify Payments availability by country, payout timing, or reserve and hold rules. We did not read Shopify’s current rates for markets outside the US or its contract terms for Plus. We did not verify any gateway’s rates other than Stripe’s online card rate. We read the US pricing page from a US connection and found the figures unchanged.