Finding the best Shopify payment provider can have a significant impact on your store’s profitability, checkout experience, and long-term growth; but not all deliver the same experience for merchants or customers. Differences in processing fees, payment methods, international coverage, and payout speed can have a measurable effect on conversion rates and operating costs. This guide provides a comprehensive comparison of the leading Shopify payment providers, highlighting their strengths, limitations, and ideal use cases so you can make a more informed decision for your store.
What are Shopify payment providers?
A Shopify payment provider (also called a payment gateway) is the service that processes your customers’ payment information and transfers the resulting funds to your bank account. Every time a customer enters their card details at checkout, the payment provider authorizes the transaction, verifies the card, and facilitates the movement of money from the customer’s bank to yours.
Payment providers connect to your Shopify store through a direct integration, either built natively into Shopify or configured through Settings > Payments in your admin. Each provider handles the technical complexity of secure payment processing so you don’t have to.
Shopify payments vs. External payment providers
The single most important thing to understand about payment provider Shopify selection is the transaction fee structure. If Shopify Payments is available in your country and you choose to use any other provider instead, Shopify charges an additional transaction fee on every sale (2.0% on Basic, 1.0% on Shopify, 0.5% on Advanced). This fee is on top of whatever the external provider charges, making third-party gateways significantly more expensive in most cases.
The only scenarios where an external provider makes financial sense are: (1) Shopify Payments is not available in your country, (2) the external provider offers a specific feature unavailable through Shopify Payments that justifies the additional cost, or (3) you’re on Shopify Plus where Shopify offers custom third-party gateway terms.
9 Best Shopify Payment Providers
1. Shopify Payments
Shopify Payments is the default recommendation for any merchant operating in a supported country, and for good reason: it’s the only provider that eliminates Shopify’s transaction fee. It’s also the only provider with deep native integration, meaning your payment data, order data, fraud analysis, and payout reports all live in one place.
- Processing fee: 2.9% + 30¢ (Basic) down to 2.4% + 30¢ (Advanced)
- Monthly fee: None (included in Shopify plan)
- Countries supported: 23+ for payouts
- Standout features: Shop Pay, Apple Pay, Google Pay, Meta Pay, Shop Pay Installments, PCI compliance, built-in fraud analysis
Best for: Any store in a supported country that wants the simplest, most cost-effective setup. The go-to starting point for 90%+ of Shopify merchants.
2. PayPal
PayPal is the world’s most recognized digital payment brand, with over 400 million active accounts globally. Many customers who hesitate to enter card details on an unfamiliar store will readily click a PayPal button because they trust the intermediary.
- Processing fee: 3.49% + a fixed fee (varies by country)
- Monthly fee: None
- Countries supported: 200+ countries for selling; 60+ for payouts
- Standout features: PayPal Pay Later, Venmo (US), strong buyer protection, widely used globally
Best for: Adding as a secondary payment option alongside Shopify Payments. Essential for international stores or markets where PayPal has high consumer penetration. Not ideal as a primary provider due to the higher combined cost.
3. Stripe
Stripe is one of the most powlerful payment platforms available, offering best-in-class APIs, extensive customization options, and support for complex payment flows including subscriptions, marketplace payouts, and custom checkout experiences. It powers Shopify Payments on the backend, but connecting it directly gives you more API control.
- Processing fee: 2.9% + 30¢ (same as Shopify Payments, but + Shopify’s transaction fee if SP is available in your country)
- Monthly fee: None
- Countries supported: 45+
- Standout features: Subscriptions, Stripe Radar (ML fraud detection), 135+ currencies, extensive developer APIs, Stripe Billing
Best for: Stores with custom development needs, subscription models, or complex payment logic. Best used in countries where Shopify Payments is unavailable.
4. Square
Square is unique among Shopify payment providers in that it’s built from the ground up for both online and in-person commerce. If you run a retail location alongside your Shopify store and want unified payment reporting across both channels, Square is the strongest option in this list.
- Processing fee: 2.6% + 10¢ online (lower than most)
- Monthly fee: None for standard plan
- Countries supported: US, UK, Canada, Australia, Japan, Ireland
- Standout features: Free POS hardware, Afterpay integration, inventory sync, unified reporting across online and in-person
Best for: Merchants with a physical retail presence who want one payment system for everything. The Afterpay integration makes it strong for fashion and lifestyle stores too.
5. Authorize.net
Authorize.net has been a stalwart of US ecommerce payment processing since 1996. It’s backed by Visa and trusted by thousands of established businesses, particularly in B2B, healthcare, and regulated industries where enterprise-grade reliability and compliance are non-negotiable.
- Processing fee: 2.9% + 30¢
- Monthly fee: $25/month (gateway fee)
- Countries supported: US, Canada, UK, Europe, Australia
- Standout features: Advanced fraud detection suite, customer profiles for recurring billing, dedicated US support, strong compliance history
Best for: Established US merchants who prioritize reliability and support over cost, particularly in regulated industries. The $25/month fee makes it less attractive for newer or lower-volume stores.
6. Klarna
Klarna is the global leader in Buy Now Pay Later, operating in 45 countries with over 150 million active users. It offers multiple payment modes — Pay Now, Pay in 30 days, Pay in 3–4 installments, and monthly financing — giving customers maximum flexibility at checkout.
- Processing fee: Custom merchant rate (typically 3–5%, varies by volume and country)
- Monthly fee: None
- Countries supported: 20+ for merchants; available to customers in 45+ countries
- Standout features: Multiple BNPL modes, Klarna app for customer loyalty, strong brand recognition in Europe and growing in North America
Best for: Stores with higher average order values (above $100) where purchase hesitation based on upfront cost is a known conversion barrier. Especially strong in fashion, electronics, and home goods.
7. Afterpay
Afterpay (known as Clearpay in the UK) is the BNPL provider most associated with fashion, beauty, and lifestyle verticals. Its split-payment model — 4 equal payments over 6 weeks — resonates strongly with 18–35 year-old female shoppers, which are the core demographic for many fashion and beauty brands.
- Processing fee: 4–6% per transaction (higher than most providers)
- Monthly fee: None
- Countries supported: US, UK, Canada, Australia, New Zealand
- Standout features: Afterpay Shop app drives discovery traffic back to your store, strong brand affinity in fashion/beauty, simple merchant integration
Best for: Fashion, beauty, and lifestyle Shopify stores with an 18–35 female-skewing demographic. The higher processing fee is offset by typically higher conversion rates and average order values for this audience.
8. 2Checkout
2Checkout, now operating under the Verifone brand, is the specialist choice for merchants who need to sell and accept payments in markets that most other providers don’t cover. It supports 200+ sell-to countries, 100+ currencies, and has strong expertise in handling cross-border payment complexity including local tax compliance and international fraud prevention.
- Processing fee: 3.5% + 35¢ (higher than US-centric providers)
- Monthly fee: None
- Countries supported: Can sell to 180+ countries; merchant payout supported in fewer
- Standout features: 100+ currencies, built-in tax compliance for global selling, subscription management, local payment method support by region
Best for: Merchants whose primary growth strategy is international expansion, especially into markets underserved by Shopify Payments, PayPal, and Stripe.
9. Amazon Pay
Amazon Pay allows customers to pay using the payment and shipping details stored in their Amazon account — no new account creation, no card entry, no friction. For stores targeting an audience that shops heavily on Amazon (which is most of the US), the trust factor and convenience of Amazon Pay can meaningfully lift checkout conversion.
- Processing fee: 2.9% + 30¢ (standard ecommerce rate)
- Monthly fee: None
- Countries supported: US, UK, Germany, France, Italy, Spain, Japan, and more
- Standout features: Zero new account creation for Amazon customers, Alexa voice shopping potential, strong fraud protection backed by Amazon
Best for: US-focused stores selling consumer goods to an audience that already shops on Amazon. Works especially well as a secondary payment option alongside Shopify Payments.
Choosing the best payment provider for Shopify
The right payment provider Shopify merchants need varies significantly based on business size, geography, and product type. Use this decision matrix to narrow down your options:
| Situation | Best Provider | Reason |
| Shopify Payments available in your country | Shopify Payments | No extra transaction fees; all-in-one integration |
| Shopify Payments unavailable in your region | Stripe or PayPal | Strong global support; easy Shopify integration |
| Selling internationally across 50+ countries | 2Checkout + PayPal | 2Checkout supports 180+ sell-to countries; PayPal adds trust |
| High-volume ($500K+/year) | Shopify Payments (Advanced) | Lowest per-sale rate without enterprise negotiation |
| High-ticket store (AOV > $150) | Shopify Payments + Klarna | BNPL reduces purchase barrier; full card coverage |
| Omnichannel (online + retail POS) | Square | Unified online/in-person processing; single dashboard |
| Subscription / SaaS | Stripe | Best-in-class recurring billing API and Shopify app support |
| B2B / international invoicing | 2Checkout or Authorize.net | Strong B2B tooling; net terms support |
Conclusion
Choosing the best Shopify payment provider is ultimately about finding the right balance between cost, convenience, reliability, and customer experience. The ideal solution will depend on your store’s size, target audience, and growth strategy. By taking the time to evaluate your options carefully, you can select the best payment provider for Shopify store and create a smoother checkout experience that supports higher conversions and sustainable growth.
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