The Best Shopify Payment Gateways for UK Stores in 2026

A Shopify payment gateway is the provider that takes the customer’s money at checkout and passes it to your bank account, and on Shopify there are two kinds: Shopify Payments, which is built in, and everything else, which Shopify calls a third-party provider. The difference is not just features. Shopify charges a transaction fee on every order that goes through a third-party gateway, even if Shopify Payments is switched on alongside it, and that fee is 2% on the Basic plan, 1% on Grow, 0.6% on Advanced and 0.2% on Plus (Shopify Help Center). Any comparison of Shopify payment gateways for a UK store that leaves that fee out is comparing the wrong numbers, which is what most of them do.

This page compares the five gateways UK stores actually choose between, with the Shopify fee included, on a store taking £100,000 a month across 2,000 orders. The rates are the providers’ published UK rates on 25 September 2026; all are ex VAT.

The five, in one table

1. Shopify Payments

Shopify Payments is the default for a reason. It is switched on in a few clicks, it carries no Shopify transaction fee, it supports Apple Pay, Google Pay and Shop Pay, and its card rate falls with your plan: 2% + 25p on Basic, 1.7% + 25p on Grow, 1.5% + 25p on Advanced and 1.3% + 25p on Plus for standard UK cards (Shopify UK pricing). Amex and international cards cost more (3.1% + 25p on Basic down to 2.3% + 25p on Plus), and since Brexit Shopify classifies EU cards as international. Payouts in the UK take a minimum of three business days, plus whatever your bank adds. It runs on Stripe’s infrastructure, which matters for the Stripe question below. For a UK store, treat Shopify Payments as the card baseline every other gateway has to beat after Shopify’s fee is added.

2. Atoa (Pay by Bank)

Atoa adds Pay by Bank to the Shopify checkout: the customer picks their bank, approves the payment with Face ID or a fingerprint in their own Bank app, and the money moves account to account over Faster Payments, with Atoa paying out to your business account within 48 hours. There is no card in the transaction, so there is no interchange, no scheme fee and no chargeback; a customer who is owed money asks for a refund, which you send from the Atoa dashboard, and the order syncs to Shopify like any other. Atoa is authorised by the FCA for payment initiation (FRN 1007647), ISO 27001 and SOC 2 certified, and available on the Shopify App Store to UK registered limited companies as two apps, one for Pay by Bank and one for card.

The rate is 0.7% + 20p ex VAT online, falling with volume, and no Shopify transaction fee applies to Atoa Pay by Bank orders, so on every plan it lands below Shopify Payments’ card rate: £1,100 a month in the example below against £1,800 to £2,500. Atoa’s card app takes Visa, Mastercard, Amex, Apple Pay and Google Pay from 1.3% + 20p; it exists so a store can run one provider for bank and card. Setup and the app links are on Atoa’s Shopify page.

3. Stripe

Stripe’s published UK rate is 1.5% + 20p for standard UK cards, 2.5% + 20p for EEA cards and 3.15% + 20p for other international cards, plus 2% where currency conversion is needed, with no monthly fee (Stripe UK pricing). Its strengths are the developer tooling, Billing for subscriptions, Radar for fraud and 135-plus currencies. On Shopify, though, Stripe direct carries the third-party fee that Shopify Payments (which runs on Stripe) does not, so for a UK-only store it is usually the same rails at a higher total. It earns its place for stores that already run Stripe across other channels and want one dashboard, or that need features Shopify Payments does not expose.

4. PayPal

PayPal is pre-installed on every Shopify store and is the one third-party option Shopify exempts from its transaction fee when Shopify Payments is active. UK fees are 2.9% + 30p for payments funded from a PayPal balance or account and 1.2% + 30p for card payments taken through PayPal’s checkout (PayPal UK merchant fees). Funds land in your PayPal balance immediately and reach your bank in about a business day. It is expensive as a primary gateway but converts a slice of customers who will not type a card number, which is why most UK stores keep it as a second button rather than the first.

5. Adyen

Adyen prices every payment as a fixed $0.13 processing fee plus a method fee: Interchange++ plus 0.60% for Visa and Mastercard, 3.95% for Amex outside North America, $0.13 + €0.50 for UK open banking (Adyen pricing). There are no setup or monthly fees but there is a minimum invoice, and pricing is quoted per business. It is a single integration for online, in-app and in-store across 60-plus countries, with its own acquiring and risk tools, and it is built for brands with a payments team to run it. For a UK store on Advanced or Plus trading in several countries it is the serious alternative to Shopify Payments; for a domestic store it is more platform than the job needs.

What each one costs on £100,000 a month

The example is 2,000 UK card or bank payments averaging £50, all standard UK debit and credit cards, with Shopify’s third-party fee added where it applies. Amex, international cards and currency conversion would raise every card row.

Three things fall out of the table. Shopify Payments is the right card gateway on every plan; nothing beats it on cards once the third-party fee is in. Pay by Bank is the cheapest row on every plan, at £1,100 a month against Shopify Payments’ £1,800 to £2,500, and it carries no chargebacks, which on cards cost the disputed amount plus a fee and on Pay by Bank do not exist. And the plan you are on is a bigger lever on the total than the gateway you pick: a Basic store paying £2,500 a month in card fees would save more by moving to Grow than by changing provider. Our guide to reducing Shopify transaction fees covers the plan side.

How to choose

If you sell mainly to UK customers, keep Shopify Payments for cards and put Pay by Bank in front of it for the customers who will use it; the saving and the removal of chargebacks are real on every plan. If you sell across several countries or need subscription billing, Stripe or Adyen bring tools Shopify Payments does not, and you pay Shopify’s fee for the privilege. Keep PayPal as a second option, not a first. And check your plan before you check your gateway. To see the numbers on your own store, book a demo or install from Atoa’s Shopify page.

Frequently asked questions

What is the best payment gateway for Shopify in the UK?

For cards, Shopify Payments, because it carries no Shopify transaction fee and its rate falls with your plan to 1.3% + 25p on Plus. For lower fees and no chargebacks on UK orders, add Atoa Pay by Bank alongside it at 0.7% + 20p ex VAT; Shopify’s third-party fee does not apply to Atoa Pay by Bank, so on every plan it costs less than Shopify Payments’ card rate.

Does Shopify charge a fee for using a third-party payment gateway?

Yes. Shopify charges 2% on Basic, 1% on Grow, 0.6% on Advanced and 0.2% on Plus on orders processed through most third-party gateways, and the fee applies even when Shopify Payments is active. PayPal, manual payment methods and Atoa Pay by Bank are not charged this fee.

Can I use Stripe as a payment gateway on Shopify in the UK?

Shopify Payments already runs on Stripe’s infrastructure, so for a UK store the practical choice is Shopify Payments, which has no Shopify transaction fee, over Stripe direct, which does. Stripe direct makes sense if you already run Stripe across other channels or need Stripe Billing or Radar.

How long do Shopify Payments payouts take in the UK?

The minimum settlement time is three business days after the order, and new accounts start on a longer schedule. Your bank then takes one to three business days to post the deposit. Atoa Pay by Bank pays out to your business account within 48 hours.

Is there a free payment provider for Shopify?

No gateway is free of transaction fees. Shopify Payments has no monthly or setup fee but charges per transaction, Stripe and Atoa have no monthly fee for their Shopify apps, and every third-party provider also attracts Shopify’s plan-based transaction fee.

Do Pay by Bank payments on Shopify have chargebacks?

No. A Pay by Bank payment is approved by the customer in their own Bank app and moves account to account, so there is no card scheme to run a chargeback. Customers can still request a refund, which you issue from the Atoa dashboard and which syncs to the Shopify order.

Sources

• Shopify, UK pricing (plan prices, online card rates, third-party transaction fees), 25 September 2026
• Shopify Help Center, Third-party payment providers
• Shopify Help Center, Payouts and settlement times in the United Kingdom
• Stripe, UK pricing
• PayPal, UK merchant fees
• Adyen, Pricing
• Atoa, Shopify and pricing pages