Best Payment Gateway for Ecommerce Stores
Why Your Ecommerce Platform Matters
Your ecommerce platform dictates which payment gateways work best because of how deeply the platform integrates with each processor. Native integrations mean your payment data, order data, and customer data live in one system. Third-party integrations work but often create gaps in reporting, require extra plugins, and add maintenance overhead.
Shopify has its own payment system (Shopify Payments, powered by Stripe) and penalizes merchants who use other gateways with a 0.6% to 2% surcharge. WooCommerce is open and supports dozens of gateways through plugins, but WooCommerce Payments (also powered by Stripe) provides the tightest integration. BigCommerce does not charge surcharges on any gateway and has preferred partnerships with PayPal and Stripe. Squarespace uses Stripe as its built-in processor with no alternative options.
The first question when choosing a payment gateway is always "which platform am I on?" because the answer narrows your best options immediately.
1. Shopify Payments: Best for Shopify Stores
Shopify Payments charges 2.9% + 30 cents on Basic ($39/month plan), 2.6% + 30 cents on Shopify ($105/month plan), and 2.4% + 30 cents on Advanced ($399/month plan). These rates are competitive, but the real value is avoiding Shopify's third-party gateway surcharge. If you use any other payment processor on Shopify, the platform adds 2%, 1%, or 0.6% on top of whatever your gateway charges.
For a store on the Basic plan processing $20,000 per month through a third-party gateway, the surcharge alone costs $400 per month, or $4,800 per year. That surcharge disappears when you use Shopify Payments. Unless you operate in a country where Shopify Payments is not available or your business category is not supported, there is no financial reason to use an external gateway on Shopify.
Shopify Payments includes Shop Pay, Shopify's accelerated checkout that stores customer payment and shipping information for one-click purchases. Shop Pay has been shown to increase checkout conversion rates by up to 50% compared to standard checkout flows, because returning customers can complete their purchase in seconds.
2. Stripe: Best Standalone Gateway for Any Platform
Stripe charges 2.9% + 30 cents for domestic online transactions with no monthly fees. It integrates with Shopify (as the engine behind Shopify Payments), WooCommerce, BigCommerce, Squarespace, Wix, Magento, PrestaShop, and virtually every other ecommerce platform through official plugins or third-party integrations.
For ecommerce stores specifically, Stripe's relevant features include Stripe Checkout (a conversion-optimized hosted payment page), adaptive payment methods that show different options based on the customer's location, built-in support for Apple Pay and Google Pay, automatic tax calculation with Stripe Tax, and Stripe Radar for fraud prevention. The hosted checkout page handles all PCI compliance requirements, meaning card data never touches your server.
Stripe's subscription billing (Stripe Billing) is the strongest in the industry for ecommerce stores selling subscription boxes, memberships, or recurring product shipments. It handles proration, trial periods, coupons, metered usage, and smart retry logic for failed payments automatically. The customer portal lets subscribers manage their own plans, update payment methods, and view invoices without contacting support.
If you are on WooCommerce, BigCommerce, or a custom-built store and want a single gateway that covers every payment scenario you might encounter, Stripe is the answer.
3. PayPal: Best Secondary Gateway
PayPal charges 3.49% + 49 cents for standard PayPal Checkout and 2.99% + 49 cents for Advanced Credit and Debit Card payments. The rates are higher than Stripe and Shopify Payments, which makes PayPal expensive as a primary gateway. But PayPal's strength is not in pricing, it is in conversion.
Ecommerce stores that offer PayPal alongside their primary gateway consistently report higher checkout completion rates. The effect is strongest for stores with average order values under $100, mobile-heavy traffic, or customers in markets where PayPal has dominant consumer adoption. The PayPal brand at checkout reduces purchase anxiety for first-time buyers who have never seen your store before.
The recommended approach for ecommerce stores is to offer PayPal as a button alongside your primary checkout form, not as the only payment option. This lets cost-conscious customers pay with cards (at lower fees) while giving PayPal-loyal customers their preferred option. Most ecommerce platforms make this dual-gateway setup easy to configure.
4. WooCommerce Payments: Best for WooCommerce Stores
WooCommerce Payments is a free plugin that brings Stripe-powered payment processing directly into the WooCommerce dashboard. It charges 2.9% + 30 cents for US cards and 3.9% + 30 cents for international cards, matching Stripe's standard rates. The key advantage is dashboard integration: you manage payments, view transaction details, handle disputes, and track deposits without leaving the WooCommerce admin.
WooCommerce Payments also includes built-in support for Apple Pay and Google Pay through its express checkout buttons, multi-currency support for stores selling internationally, and subscription payment handling when paired with the WooCommerce Subscriptions plugin. Fraud protection uses Stripe Radar under the hood.
The tradeoff compared to using the standalone Stripe plugin for WooCommerce is that WooCommerce Payments is maintained by Automattic (the company behind WordPress.com), not by Stripe directly. Updates sometimes lag behind Stripe's latest features. Some merchants prefer the standalone Stripe plugin for WooCommerce because it gives access to newer Stripe features faster and allows more control over the checkout experience.
5. Authorize.net: Best for Established High-Volume Stores
Authorize.net charges a $25 monthly gateway fee plus 2.9% + 30 cents per transaction on its all-in-one pricing plan. Alternatively, you can pair Authorize.net as a gateway-only service ($25/month + 10 cents per transaction) with your own merchant account for interchange-plus pricing. The latter approach is cheaper for stores processing more than $20,000 per month.
Authorize.net has been operating since 1996 and processes payments for over 440,000 merchants. It supports all major ecommerce platforms through official and third-party plugins. The gateway offers Advanced Fraud Detection Suite (AFDS), customer payment profiles for tokenized repeat purchases, automated recurring billing, and detailed transaction reporting.
For newer small businesses, Authorize.net's monthly fee and older interface make it less attractive than Stripe or Shopify Payments. But for established ecommerce businesses processing significant volume through a merchant account with interchange-plus pricing, Authorize.net remains a reliable and cost-effective gateway.
Choosing the Right Gateway for Your Store
On Shopify: Use Shopify Payments. Add PayPal as a secondary option. Only consider alternatives if Shopify Payments is not available in your country or does not support your business type.
On WooCommerce: Use WooCommerce Payments or the Stripe plugin. Add PayPal as a secondary option. Consider Helcim or a merchant account with Authorize.net if you process more than $25,000 per month and want lower effective rates.
On BigCommerce: Use Stripe or the PayPal partnership (which offers preferred rates). BigCommerce does not charge surcharges on any gateway, so you have full freedom to choose based on features and fees.
On a custom platform: Use Stripe for the broadest feature set and best developer experience. Add PayPal for conversion. Consider Adyen or Braintree if you process at scale and need advanced features like network tokenization or intelligent payment routing.
Processing $50,000+ per month: Regardless of platform, request custom pricing from Stripe (available through Stripe's sales team for high-volume merchants) or evaluate interchange-plus pricing through Helcim, Payment Depot, or a traditional merchant account with Authorize.net as the gateway.