ComparePSP

Best Payment Gateway for Shopify (2026)

Compare the top payment gateways for Shopify stores in 2026. We rank them by Shopify integration quality, transaction fees, checkout conversion, and additional payment method support.

What to Look For

  • Total cost including Shopify surcharges
  • Native Shopify integration quality
  • Checkout conversion optimization
  • Payment method breadth
  • Shopify POS compatibility
  • Subscription and recurring billing support

Top Picks at a Glance

#ProviderRatingTransaction FeeMonthly FeeBest For
1Stripe logoStripe4.62.9% + $0.30$0Best for developer-first companies building custom payment experiences
2PayPal logoPayPal4.02.99% + $0.49$0 (standard) / $30 (Pro)Best for businesses wanting instant brand recognition and buyer trust
3Mollie logoMollie4.2€0.25 + scheme rate (1.8% EU / 2.8% non-EU cards)$0Best for European small businesses seeking easy setup and local payment methods
4Adyen logoAdyen4.5Interchange++ (€0.11 processing + scheme fee + interchange)$0Best for enterprise businesses needing unified global payment infrastructure

Full Rankings

#1
Stripe logo

Stripe

4.6
4.6 / 5.0

Transaction fee: 2.9% + $0.30

Why it's good

Stripe powers Shopify Payments, making it the most natural and cost-effective payment gateway for Shopify stores. When you activate Shopify Payments, you are using Stripe's infrastructure with zero additional transaction fees from Shopify. Card rates start at 2.9% + $0.30 on the Basic plan and decrease with higher Shopify plans. The integration is seamless — payments, refunds, and reporting all live within the Shopify admin. Shopify Payments supports Apple Pay, Google Pay, and Shop Pay (which boasts a 91% higher conversion rate than regular checkout).

Why it might not be

Shopify Payments (Stripe) is not available in all countries — merchants in unsupported regions need an alternative. Certain business categories are prohibited. You cannot customize the payment flow or access Stripe's advanced features (Radar rules, Sigma analytics) through Shopify Payments as you can with a direct Stripe integration. High-volume merchants may find better rates with interchange-plus pricing from other providers, even after accounting for Shopify's surcharge.

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#2
PayPal logo

PayPal

4.0
4.0 / 5.0

Transaction fee: 2.99% + $0.49

Why it's good

PayPal is the most commonly added secondary payment gateway on Shopify stores. Adding PayPal checkout alongside Shopify Payments can increase conversion by capturing customers who prefer paying with their PayPal balance, Venmo, or PayPal Credit. Shopify has a native PayPal integration that is easy to activate. PayPal's buyer protection builds trust for first-time customers. Pay Later options can increase average order value for higher-priced products.

Why it might not be

Using PayPal as your primary (or only) Shopify gateway triggers Shopify's additional transaction fee (0.5-2%), making the total cost very high. PayPal's own fees (2.99% + $0.49) plus Shopify's surcharge can push total processing costs above 5%. PayPal redirects customers to an external page during checkout, which can reduce conversion compared to Shopify's native checkout experience.

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#3
Mollie logo

Mollie

4.2
4.2 / 5.0

Transaction fee: €0.25 + scheme rate (1.8% EU / 2.8% non-EU cards)

Why it's good

Mollie offers a well-maintained Shopify plugin that adds European local payment methods — iDEAL, Bancontact, Klarna, SOFORT, and more — to your Shopify checkout. For European Shopify stores, Mollie fills the gap where Shopify Payments may not support all local methods. The integration is straightforward, and Mollie's transparent pricing with no monthly fees appeals to cost-conscious merchants.

Why it might not be

Using Mollie on Shopify triggers the additional Shopify transaction fee (0.5-2% on top of Mollie's own fees). Mollie is limited to European markets. The Shopify integration, while functional, is not as deeply embedded as Shopify Payments — some features like Shopify POS integration may be limited. For most European Shopify stores, Shopify Payments is still the better primary gateway.

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#4
Adyen logo

Adyen

4.5
4.5 / 5.0

Transaction fee: Interchange++ (€0.11 processing + scheme fee + interchange)

Why it's good

Adyen offers a Shopify integration suitable for high-volume Shopify Plus merchants. Its interchange-plus pricing can be more cost-effective at scale, and its broad payment method support (250+ methods) gives enterprise Shopify stores maximum flexibility. Adyen's authorization rate optimization helps large stores recover revenue from declined transactions.

Why it might not be

Adyen's Shopify integration triggers the additional Shopify transaction fee, and the interchange-plus savings must overcome this surcharge to break even. Adyen requires minimum volumes and a sales process, making it impractical for most Shopify stores. The integration is designed for Shopify Plus merchants only. Setup is complex compared to activating Shopify Payments.

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Choosing a payment gateway for your Shopify store involves a unique consideration that does not apply to other ecommerce platforms: Shopify charges an additional transaction fee (0.5-2% depending on your plan) when you use any external payment gateway instead of Shopify Payments. This fee fundamentally shapes the decision, because it means using a third-party gateway must deliver enough value to justify the additional cost. Shopify Payments, powered by Stripe's infrastructure, is the default and most cost-effective option for the majority of Shopify merchants. It eliminates the additional transaction fee, integrates seamlessly with the Shopify checkout, and provides a unified experience for payments, refunds, and reporting within the Shopify admin. However, Shopify Payments is not available in all countries, does not support all business types (it has a restricted businesses list), and may not offer the best rates for high-volume merchants. For stores where Shopify Payments is unavailable or unsuitable, choosing the right alternative gateway requires careful consideration of the total cost including Shopify's surcharge, the gateway's own fees, checkout experience quality, supported payment methods, and how well the gateway integrates with Shopify's ecosystem. Some merchants also add a secondary payment gateway alongside Shopify Payments to offer additional payment options like PayPal, buy now pay later, or local payment methods that Shopify Payments does not support in their region. We evaluated the leading payment processors on criteria specific to Shopify merchants: total cost of ownership (including Shopify surcharges), native integration quality, checkout conversion impact, payment method breadth, and compatibility with Shopify's subscription and POS features.

Related Resources

Provider

Stripe

Provider

PayPal

Provider

Mollie

Provider

Adyen

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Method

Visa / Mastercard

Method

American Express

Method

Apple Pay

Method

Google Pay

Method

SEPA

Method

ACH

Method

iDEAL

Method

Bancontact

Method

Sofort (Klarna)

Method

Giropay

Method

Alipay

Method

WeChat Pay

Method

Klarna (Buy Now, Pay Later)

Method

Affirm

Method

Afterpay (Block)

Method

EPS

Method

Przelewy24

Method

BLIK

Method

Multibanco

Method

Paysafecard

Method

PIX

Method

Boleto Bancário

Method

UPI

Method

GrabPay

Frequently Asked Questions

Should I use Shopify Payments or a third-party gateway?
For most Shopify merchants, Shopify Payments (powered by Stripe) is the best choice. It eliminates the 0.5-2% additional transaction fee that Shopify charges for external gateways, integrates natively with the checkout, and provides unified reporting. Use a third-party gateway only if: Shopify Payments is not available in your country, your business type is restricted by Shopify Payments, or you process enough volume that interchange-plus pricing saves more than the Shopify surcharge costs.
What is the Shopify transaction fee for external gateways?
Shopify charges an additional transaction fee when you use any payment gateway other than Shopify Payments: 2% on the Basic plan ($39/month), 1% on the Shopify plan ($105/month), and 0.5% on the Advanced plan ($399/month). This fee is in addition to the gateway's own processing fees. On Shopify Plus, this fee can be negotiated. This surcharge is the primary reason most merchants use Shopify Payments.
Can I use multiple payment gateways on Shopify?
Yes. Shopify allows one primary gateway (ideally Shopify Payments) plus additional manual and alternative payment methods. The most common setup is Shopify Payments as the primary gateway with PayPal added as an alternative. You can also add buy now pay later providers (Klarna, Afterpay), local payment methods through gateways like Mollie, and manual payment methods like bank transfers or cash on delivery.
Is Shopify Payments the same as Stripe?
Shopify Payments is built on Stripe's infrastructure but is not the same as having a direct Stripe account. Shopify Payments offers a simplified version of Stripe integrated directly into the Shopify admin. You do not get access to Stripe's dashboard, advanced Radar fraud rules, Sigma analytics, or the full Stripe API. However, the payment processing, security, and reliability are powered by Stripe's technology.
What are the best Shopify payment methods to increase conversion?
Enable Shop Pay — Shopify's accelerated checkout — which stores customer details and has a 91% higher conversion rate than guest checkout. Add Apple Pay and Google Pay for mobile shoppers. Include PayPal for customers who prefer it. For higher-priced products, add a buy now pay later option (Klarna, Afterpay, or Shop Pay Installments). In European markets, add local payment methods relevant to your target countries through Shopify Payments or Mollie.