Reviewed November 9, 2026

Shopify Payments vs a Third-Party Gateway: The Fee Math Before You Choose

On the Basic plan, Shopify Payments charges 2.9% plus 30 cents per online transaction, and no extra fee. A third-party gateway charges its own processing fee plus Shopify's additional transaction fee: 2% on Basic, 1% on the Shopify plan, 0.6% on Advanced, 0.2% on Plus. On a 100 dollar order on Basic, that is 3.20 dollars against 5.20 dollars. The gap is the decision.

A merchant choosing a payment gateway usually starts with loyalty: they already use Stripe, or their accountant likes Authorize.net, or PayPal is what their customers expect. Loyalty is the wrong place to start. The fee math is the place to start, because the gap is not small and it compounds on every order.

The structure is simple. Shopify Payments charges only the card processing rate for your plan. A third-party gateway charges its own processing fee plus Shopify's additional transaction fee on top. On the Basic plan that surcharge is 2% of the order, and it applies to every transaction that does not run through Shopify Payments.

The rate card, plan by plan

On Basic, 39 dollars a month, Shopify Payments charges 2.9% plus 30 cents for online card payments. The third-party gateway surcharge on the same plan is 2%. On the Shopify plan, 105 dollars a month, the card rate drops to 2.7% plus 30 cents and the surcharge drops to 1%. On Advanced, 399 dollars a month, it is 2.5% plus 30 cents and a 0.6% surcharge. On Plus, the card rate is negotiated and the surcharge is 0.2%.

Work it through on a 100 dollar order on Basic. Shopify Payments costs 3.20 dollars. A third-party gateway charging the standard 2.9% plus 30 cents costs 3.20 to the gateway plus 2.00 to Shopify, a total of 5.20 dollars. That is a 62% cost increase for the same transaction, and it repeats on every order, every day, for as long as the gateway stays connected.

At 50,000 dollars a month in sales, the third-party gateway on Basic costs about 1,025 dollars more than Shopify Payments. Over a year that is more than 12,000 dollars. The gap narrows on higher plans, 450 dollars a month on Plus, but it never closes, because the surcharge never reaches zero on any plan.

When a third-party gateway still wins

The surcharge is not the whole story. Shopify Payments is not available in every country, and a merchant where it is unavailable cannot avoid the surcharge on any plan. For those merchants the comparison is between gateways, not between Shopify Payments and a gateway, and the cheapest gateway wins on its own rate.

Some merchants need a gateway feature Shopify Payments does not offer: a specific fraud tool, a processor relationship their bank requires, or support for a payment method their customers demand. A gateway that brings in customers Shopify Payments cannot serve is worth its fee. A gateway that duplicates what Shopify Payments already does is not.

PayPal has a carve-out worth knowing. With Shopify Payments active, PayPal payments are excluded from the third-party fee. On Plus, third-party fees are waived for all other payment methods when Shopify Payments is the primary gateway. The exceptions are narrow, but they change the math for stores where PayPal is a large share of checkout.

The decision, in order

First, check whether Shopify Payments is available in your country. If it is not, the decision is made for you: pick the cheapest reliable gateway and move on. If it is available, the default is Shopify Payments, and the burden of proof is on the alternative.

Second, run the math on your actual volume, not on a hypothetical. Take last month's sales, apply both fee structures, and look at the monthly difference. A 200 dollar monthly gap is a rounding error for some stores and a hire for others. The number decides, not the brand.

Third, check the exceptions. International transactions add 1.5% through Shopify Payments for US stores, plus another 1.5% if currency conversion is involved. A store with heavy international volume should run that math too, because the surcharge comparison changes when the international fees are included. The gateway that is cheaper domestically is not always cheaper globally.

Frequently asked questions

What is Shopify's third-party transaction fee?

It is a surcharge Shopify adds when you process payments through a gateway other than Shopify Payments. On Basic it is 2% of the order, on the Shopify plan 1%, on Advanced 0.6%, and on Plus 0.2%. It applies on top of whatever the gateway itself charges.

Does using PayPal trigger the third-party fee?

Not if Shopify Payments is active. PayPal payments are excluded from the third-party fee when Shopify Payments is activated. On Plus, third-party fees are waived for all other payment methods when Shopify Payments is the primary gateway.

Is Shopify Payments available in my country?

Shopify Payments is available in 23 countries. If your country is not on the list, you cannot use it and cannot avoid the third-party surcharge. Check Shopify's availability list for your country before comparing rates.

Do international transactions cost extra through Shopify Payments?

Yes. For US stores, Shopify Payments charges an additional 1.5% on international transactions, plus a separate 1.5% currency conversion fee when conversion is involved. Run the math on your international volume before deciding, because it changes the comparison.