Stripe vs Shopify Payments: Which Is Better in 2026?

At a glance

	Stripe	Shopify Payments
Best for	Most online stores and custom checkouts	Stores built on Shopify
Online card rate	2.9% + 30¢ (domestic cards)	2.9% + 30¢ Basic, 2.7% + 30¢ Grow, 2.5% + 30¢ Advanced
Monthly fee	None	None beyond your Shopify plan (Basic $39 / month, $29 billed yearly)
International cards	+1.5%, plus 1% if currency conversion applies	Varies by plan and card type
Platform support	Most ecommerce platforms and custom builds	Shopify stores only
Setup	Account plus integration; custom builds need a developer	Built in, turned on inside Shopify admin
Disputes	$15 fee per dispute	Handled inside Shopify admin
Extra products	Billing 0.7%, Tax from 0.5%, advanced Radar fraud tools	Shop Pay, multi-currency selling, dispute tools
Accelerated checkout	Link, Apple Pay, Google Pay	Shop Pay, Apple Pay, Google Pay

Shopify Payments is the better fit for stores built on Shopify, while Stripe suits stores on every other platform, custom and headless checkouts, and businesses that need subscriptions or invoicing outside a single store. In practice, your platform usually makes the choice for you. The real question is whether Shopify plus Shopify Payments, or another setup with Stripe, fits how you sell.

Both charge 2.9% plus 30 cents on a standard domestic online card payment at the entry level, so the headline rate is a tie. The differences are in where each one works, what it costs as you grow, and what you can build on top.

Where each one works

Shopify Payments only works inside Shopify. It is turned on from the Shopify admin, payouts and disputes live in the same dashboard as your orders, and there is no separate account to manage. In supported countries, Shopify does not let you connect your own Stripe account as the main card processor, and it adds a transaction fee when a store uses an outside payment provider.

Stripe works almost everywhere else. It plugs into WooCommerce, BigCommerce, and most other ecommerce platforms, and its APIs power custom and headless storefronts, marketplaces, and apps. If you sell through a website, an app, and invoices, Stripe can run all of them from one account.

Winner: depends on your platform. On Shopify, Shopify Payments wins by default. Off Shopify, Stripe is the stronger choice.

Fees and total cost

Stripe charges 2.9% plus 30 cents per successful domestic card payment, with no monthly or setup fee. International cards add 1.5%, and currency conversion adds 1%. Disputes cost $15 each. Stripe Billing costs 0.7% of billing volume on pay-as-you-go, Stripe Tax starts at 0.5% per transaction on the no-code option, and advanced Radar fraud tools start at $0.05 per screened transaction.

Shopify Payments rates fall as your Shopify plan rises: 2.9% plus 30 cents on Basic, 2.7% plus 30 cents on Grow, and 2.5% plus 30 cents on Advanced, with higher rates for business and American Express cards. There is no separate processor fee, but you need a Shopify plan, and Basic costs $39 a month or $29 billed annually. If you run Shopify Payments alongside a third-party provider, Shopify charges its own methods at standard rates plus a 1.25% premium.

Here is how that plays out on a single order. A $100 domestic card sale costs $3.20 on Stripe’s standard rate and $3.20 on Shopify Payments Basic. On Grow, the same sale costs $3.00, and on Advanced it costs $2.80. If that buyer pays with a card issued abroad, Stripe adds $1.50 more. Multiply those differences by a year of orders before you decide.

At the same volume on Shopify’s Advanced plan, Shopify Payments undercuts Stripe’s standard rate. Stripe can close that gap with custom pricing once volume is large.

Winner: Shopify Payments for Shopify stores. Lower rates on higher plans and no outside-provider fees make it cheaper there. Stripe wins on cost for everyone else, since it carries no platform fee at all.

Checkout and payment methods

Shopify Payments gives you Shop Pay, Shopify’s accelerated checkout, along with wallets and multi-currency selling. For a Shopify store, the checkout is already built and tuned, and you do not touch code.

Stripe gives you hosted and embedded checkout options, its Link accelerated checkout, digital wallets, and access to more than 100 payment methods, including many local ones for international buyers. You decide how the checkout looks and behaves, which is a strength for custom builds and a cost if you lack developer time.

Shop Pay deserves a note here. Shoppers who have saved their details with Shop Pay can check out in a few taps on any Shopify store, which is a real advantage for mobile conversion. Stripe’s Link works the same way across sites that use Stripe, so both processors offer a saved-details checkout for returning buyers.

Winner: Stripe for flexibility, Shopify Payments for simplicity. Stripe offers more methods and control. Shopify Payments gives a polished checkout with no work.

Subscriptions, invoicing, and beyond the store

Stripe is a broad payments platform. Billing handles subscriptions and recurring invoices, Tax calculates sales tax where you are registered, and ACH Direct Debit costs 0.8% capped at $5, which suits large B2B orders. Businesses that sell memberships, software, services, or wholesale on invoice get all of that from the same account as their store.

Shopify Payments is focused on Shopify checkout. Subscriptions on Shopify generally run through subscription apps, which can add their own fees.

Winner: Stripe. It covers far more ways to get paid outside a single storefront.

Fraud, disputes, and security

Stripe includes basic fraud screening with payments and sells advanced Radar tools, starting at $0.05 per screened transaction, for teams that want custom rules and reviews. Disputes cost $15 each, and Stripe’s dashboard walks you through submitting evidence. Because Stripe sits outside your store platform, you may need to pull order and tracking details from another system to build a strong response.

Shopify Payments handles disputes inside the Shopify admin, next to the order, the customer record, and the tracking number. That makes evidence easier to gather for a small team. Shopify’s order screens also flag risky orders before you ship, which helps you cancel likely fraud before the goods leave.

On security, both providers keep raw card numbers off your servers when you use their checkout or payment fields, so your PCI compliance work stays light either way. Custom Stripe card forms raise that burden, which is another reason to use its hosted or embedded options.

Winner: Shopify Payments for Shopify stores. Having disputes and order data in one place saves real time. Stripe wins for teams that want deeper, tunable fraud rules.

Setup, ease of use, and support

Shopify Payments is the easiest processor to start with. You turn it on in your admin, add bank details, and you are taking payments. Refunds, disputes, and payouts sit next to the orders they belong to, and support comes from Shopify.

Stripe is easy on platforms with an official plugin, but a custom build needs a developer. Its documentation is excellent, and its dashboard is clear, but you manage a separate account and reconcile payouts against orders in another system.

Winner: Shopify Payments. Nothing beats a processor that is already built into your store.

Payouts and reporting

Stripe pays out on a rolling, weekly, or monthly schedule at no cost, and instant payouts cost 1.5% of the payout with a 50-cent minimum. Its reports are detailed and export cleanly to accounting tools. Shopify Payments shows payouts and fees inside Shopify, which makes matching sales to deposits simple for a single store.

Winner: tie. Stripe offers more payout control, and Shopify Payments makes reconciliation easier for Shopify-only sellers.

Which one should you pick?

Pick Shopify Payments if your store runs on Shopify, since it costs less there, needs no setup, and avoids outside-provider fees. Pick Stripe if you sell on WooCommerce, BigCommerce, or a custom site, or if you need subscriptions, invoicing, or payments across several products from one account. Most stores should still add PayPal as a second button either way. To compare more options, including Square, Braintree, and Adyen, see our ranked list of the best payment processors for ecommerce.

Pros and cons

Stripe

Shopify Payments

Which should you choose?

Frequently asked questions