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Best Shopify Payment Alternatives UK 2026

Updated July 2026

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UK e-commerce businesses often start on Shopify but quickly find that Shopify Payments charges transaction fees of up to 2% on top of processing costs when you use a third-party gateway. If you process £20,000 a month, that surcharge alone costs £400 every month. There are better-priced alternatives that integrate cleanly with your store and settle funds faster.

Key Takeaways

  • ✔ Shopify Payments charges 0.5% 2% extra on every transaction if you use a third-party gateway. Switching provider can eliminate that cost entirely.
  • ✔ Stripe processes payments directly via its own Shopify app at 1.4% + 20p for European cards, with no additional Shopify transaction fee.
  • ✔ PayPal Braintree charges 1.9% + 30p for standard UK card transactions and integrates natively with Shopify without triggering Shopify's third-party surcharge.
  • ✔ Square for e-commerce charges 1.9% per online transaction with no monthly fee, making it a strong option for lower-volume sellers under £5,000 a month.
  • ✔ Mollie charges 1.2% + 25p for UK and European Visa and Mastercard transactions and supports 25-plus local payment methods across Europe, useful for cross-border sellers.

Who Is This Page For

This page is for UK-based online store owners who use Shopify or are considering it, and want to understand which payment gateway gives them the lowest total cost. It covers businesses turning over between £2,000 and £100,000 a month online. If you sell internationally, run a subscription model, or want to avoid Shopify's own transaction fees, the comparisons below are directly relevant to you.

What Does an E-commerce Business Need from an Online Payment Gateway?

An online store needs a gateway that integrates without triggering Shopify's additional transaction fee. Shopify charges 0.5% on the Advanced plan, 1% on Shopify plan, and 2% on Basic plan for any gateway other than Shopify Payments. Some gateways, including Stripe and PayPal Braintree, are exempt from this surcharge under Shopify's approved partner programme. That single factor can save a Basic plan merchant £200 a month on £10,000 in sales.

Beyond fees, you need fast settlement, reliable fraud tools, and checkout conversion. Settlement speed matters: Stripe typically deposits funds by the next working day, whilst some gateways hold funds for three to five days. Checkout abandonment rises sharply with extra steps, so a gateway that supports one-click payments, Apple Pay, and Google Pay directly in the Shopify checkout is worth paying a small premium for.

Fee Comparison: Best Shopify Payment Alternatives for UK E-commerce

Provider Transaction Fee (UK Cards) Monthly Cost Verdict
Stripe 1.4% + 20p (European cards); 2.9% + 30p (non-European) £0 Best all-round for Shopify; no extra Shopify transaction fee
PayPal Braintree 1.9% + 30p for UK card transactions £0 Strong buyer trust; no Shopify surcharge; good for high-volume sellers
Square Online 1.9% per online transaction £0 Simple flat rate; best for low-volume sellers; limited international reach
Mollie 1.2% + 25p for Visa and Mastercard £0 Lowest per-transaction rate; ideal for EU cross-border sales; smaller UK presence

Our Top Pick for Shopify E-commerce: Stripe

Stripe is the strongest Shopify payment alternative for most UK online businesses. It charges 1.4% + 20p for UK and European personal Visa and Mastercard cards, and it does not trigger Shopify's third-party transaction surcharge. A Shopify Basic merchant processing £15,000 a month saves £300 a month in Shopify surcharges alone by switching from a non-exempt gateway to Stripe.

The integration is straightforward. Stripe's Shopify app installs in minutes and supports Apple Pay, Google Pay, and card payments directly in the checkout without redirecting buyers to an external page. Settlement is typically next working day into your UK bank account. Stripe's radar fraud tools are included at no extra cost and blocked over 300 million fraudulent transactions in 2023 according to the company's own published data.

The honest downside is that Stripe's pricing rises to 2.9% + 30p for non-European cards. If a large share of your customers are in the US or Australia, that rate is less competitive than some specialist international gateways. Stripe also has no UK phone support; all help is via chat and email. Read the full Stripe UK review on Compare Card Fees for a complete breakdown of fees and contract terms.

Runner-Up Options

PayPal Braintree

PayPal Braintree charges 1.9% + 30p for standard UK card transactions and is exempt from Shopify's third-party gateway surcharge. Its biggest advantage is buyer trust: research by PayPal published in 2022 found that checkout conversion increased by up to 28% when PayPal was offered as a payment option. Braintree supports recurring billing natively, making it a solid choice for subscription boxes or membership sites built on Shopify.

The weakness is that Braintree's dashboard is less intuitive than Stripe's, and the developer documentation is harder to follow for non-technical merchants. Refunds can take five to seven working days to reach customers, which generates more support queries than Stripe's typical two-to-three-day refund window. See the full PayPal Braintree review on Compare Card Fees before committing.

Mollie

Mollie charges 1.2% + 25p for UK and European Visa and Mastercard transactions, which is the lowest per-transaction rate of any major Shopify-compatible gateway in this comparison. There is no monthly fee and no minimum volume. For a store turning over £20,000 a month on UK and European cards, Mollie saves roughly £40 a month compared with Stripe on transaction fees alone.

Mollie's UK market presence is smaller than Stripe's or PayPal's, and its Shopify app has fewer reviews and less community documentation. It does trigger Shopify's third-party transaction fee, so you need to factor that cost back in. On the Shopify Advanced plan at 0.5%, processing £20,000 a month adds £100 to your bill, which erases much of the per-transaction saving. Mollie suits Advanced plan merchants or those who have negotiated away Shopify's surcharge through a Shopify Plus subscription. Read the Mollie UK review on Compare Card Fees for the full picture.

How Compare Card Fees Can Help

Compare Card Fees is a free, independent advisory service that has helped UK businesses find better card payment deals since 2012. If you are unsure which gateway fits your Shopify store's volume, product type, or customer geography, our advisers can review your current setup and identify where you are overpaying. There is no obligation and no fee for the service.

Frequently Asked Questions

What is the cheapest payment gateway for Shopify UK?

Stripe is typically the cheapest overall for UK merchants because it charges 1.4% + 20p for European cards and does not trigger Shopify's third-party transaction surcharge. Mollie has a lower per-transaction rate at 1.2% + 25p, but it does attract the Shopify surcharge on lower-tier plans, which can make it more expensive in total.

Does using a third-party gateway on Shopify always incur an extra fee?

No, not always. Shopify exempts certain approved partners, including Stripe and PayPal Braintree, from its third-party transaction fee. Any gateway not on Shopify's exempt list will incur an additional fee of 0.5% on Advanced, 1% on Shopify, and 2% on Basic. Always check Shopify's current partner list before choosing a gateway.

How quickly does Stripe settle funds for UK Shopify stores?

Stripe typically settles funds into your UK bank account the next working day after a transaction is processed. New accounts may face a two-to-seven-day rolling reserve period for the first few weeks. Once your account is established, next-day settlement is standard for the vast majority of UK merchants.

Can I use PayPal Braintree for subscription billing on Shopify?

Yes. PayPal Braintree supports recurring billing natively and integrates with Shopify subscription apps such as Recharge and Bold Subscriptions. It charges 1.9% + 30p per UK card transaction with no additional Shopify surcharge. It is a practical choice for subscription box businesses or any Shopify store with a recurring revenue model.

Is Mollie a good Shopify payment gateway for selling across Europe?

Mollie is a strong choice for cross-border European sales. It supports over 25 local payment methods including iDEAL in the Netherlands, Bancontact in Belgium, and SOFORT in Germany. Its 1.2% + 25p rate applies to UK and European Visa and Mastercard cards. The main drawback for UK-first stores is that it triggers Shopify's third-party surcharge unless you are on Shopify Plus.

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