Shopify Payments vs Stripe: Fees and What You Can Actually Use

Who it is for

Shopify store owners weighing Stripe

Time needed

20 minutes to compare

What you need

Three months of orders by card type and country

Shopify Payments vs Stripe sounds like a choice between two processors, but on Shopify it works differently. Store owners usually ask because they already use Stripe elsewhere, saw Stripe's headline rate, or want everything in one Stripe dashboard. I'm a Shopify developer and Shopify Select Partner, so I know Shopify's payment setup well, and I'll be precise about what is and isn't possible, because a lot of advice online on this topic is out of date.

Stripe's rates come from its US and UK pricing pages, and the Shopify rules from Shopify's help center and developer docs, as checked on 7 November 2026. Shopify's card rates are the ones it quotes for each plan.

The short answer

What you can and can't do with Stripe on Shopify

This is the part most comparisons get wrong, so here it is in one place:

• You can use Shopify Payments, which Stripe powers behind the scenes in its partnership with Shopify. You deal with Shopify for rates, payouts and support, not Stripe.
• You can add Stripe as a card provider through the Stripe Card Payments app in Settings > Payments. It replaced Stripe's older Shopify provider, and Stripe set a migration deadline of 31 August 2025 for stores on the old one. It supports Visa, Mastercard, American Express, Discover, Diners Club, Apple Pay and Google Pay, plus authorization, capture, void and refund. Shopify Subscriptions and subscription apps from the App Store are supported.
• It may not appear for you. Shopify decides which providers each store can choose. Stripe's own instructions say that if Stripe Card Payments doesn't show up, you can ask Stripe Support for an installation link. Neither company published a country list for it when I checked, so confirm in your admin before planning around it.
• You can't build your own Stripe integration into checkout. Shopify's developer docs say only approved partners can build payment extensions, and custom payment extensions are limited to eligible Shopify Plus merchants.
• You can use Stripe apps that don't take checkout payments, such as Stripe Subscriptions for Shopify, which manages subscriptions in Stripe while orders stay in Shopify.

Shopify Payments vs Stripe fees

Stripe's UK rate for standard UK cards looks lower than Shopify Payments on Basic. The third-party fee is what changes that. Stripe also lists a $15 fee for each dispute in the US, and instant payouts at 1.5% of the amount with a 50¢ minimum. Standard Stripe payouts are free.

In both cases Shopify Payments costs less, by $240 a month in the US example and £140 in the UK one. For Stripe to win on fees, it would need to undercut Shopify Payments by more than the third-party fee on your plan. On Basic and Grow that rarely happens at standard pricing. Check your own volumes with the Shopify fees calculator, and read my Shopify fees guide for the full list of charges.

Running Stripe next to Shopify Payments

Shopify lets a store run one direct third-party card provider alongside Shopify Payments. Its help center explains the routing, and the costs that come with it:

• Cards go to Stripe first. Shopify Payments acts as a backup and retries failed card payments. This payment recovery is always on for eligible card payments and can't be turned off.
• Recovered payments cost more. A card payment recovered through Shopify Payments is charged at the standard Shopify Payments rate plus a 1.25% premium.
• Shop Pay and local methods cost more too. Shop Pay, local payment methods and wallets Stripe doesn't offer go through Shopify Payments at the standard rate plus 1.25%.
• Wallets Stripe offers stay with Stripe, with no backup.
• Some stores can't do it. Multi-entity stores can't use it, and Plus stores on a contract need to request early access.

In practice, a mixed setup means paying the third-party fee on Stripe orders and a 1.25% premium on every Shop Pay order. If Shop Pay is a large share of your sales, as it is on many established stores, that premium adds up fast. In the US example above, if 100 of the 400 orders, worth $5,000, were paid with Shop Pay, the 1.25% premium alone would add about $62 a month.

Checkout, Shop Pay and conversion

From a conversion point of view, Shop Pay is the main reason I keep stores on Shopify Payments. It saves a shopper's details across Shopify stores, so returning Shop Pay users can pay in a couple of taps. On Shopify Payments it costs the normal card rate. With a third-party card provider, it costs 1.25% more.

Stripe's strengths, such as Stripe Checkout, Payment Links and its developer tools, mostly don't apply inside Shopify's checkout, because Shopify controls that page. What you keep with Stripe on Shopify is the processing relationship and the Stripe dashboard. That has value for a business that already runs everything through Stripe, but it doesn't make the checkout convert better. If checkout conversion is your real concern, my CRO work starts from $500 and begins with the steps shoppers actually drop out of.

Subscriptions and Stripe Billing

Subscriptions are the most common good reason to want Stripe on a Shopify store. The Stripe Subscriptions for Shopify app lets you create subscription plans, offer trials and discounts, and manage subscriptions from both Shopify and the Stripe dashboard. A few details from Stripe's docs:

• It processes recurring payments through Stripe, and can run on any subscription-supporting payment provider on Shopify, including Shopify Payments.
• Stripe's Smart Retries isn't supported when payments run through Shopify's payment platform. Standard retry schedules are.
• If a subscription moves to a Stripe-managed payment method, Shopify stops creating orders for it, which can break fulfillment set up in Shopify.

So you can keep Shopify Payments for checkout and still use Stripe Billing for subscriptions, which is often the best of both. If your subscription logic is unusual, a custom app is another route, from $800.

By country

• US: Shopify Payments Basic and Stripe both quote 2.9% + 30¢ for domestic cards, so Stripe can only cost more once the third-party fee is added. Watch the sales tax rule above.
• UK: Stripe's 1.5% + 20p for standard UK cards beats Shopify Payments Basic's 2% + 25p on rate alone, but the 2% Basic fee more than cancels it.
• EU/Netherlands: local methods like iDEAL and Bancontact would run through Shopify Payments at the 1.25% premium in a mixed setup. My Shopify Payments vs Mollie comparison covers EU payment choices.
• Australia: Shopify Payments settles in a minimum of 2 business days there. Check Stripe's Australian pricing page if you're comparing locally.
• Countries without Shopify Payments: this is where Stripe, if it's offered to your store, is a strong candidate, since every provider pays the third-party fee.

When Stripe makes sense

1. Shopify Payments isn't available for your country or business category.
2. You're on Shopify Plus with a negotiated Stripe rate low enough to cover the 0.2% fee and the Shop Pay premium.
3. Your group runs finance through Stripe across several brands or platforms and the reporting saving is worth the extra fees.
4. You only need Stripe for subscriptions, in which case use the Stripe Subscriptions app and keep Shopify Payments for checkout.

If none of these apply, Shopify Payments is the cheaper and simpler choice.

How to decide in three questions

Switching between them

1. Export three months of payments from your current provider, split by card type, wallet and country.
2. Price both setups, including the third-party fee and, for a mixed setup, the 1.25% premium on Shop Pay and local methods.
3. Check eligibility in Settings > Payments: whether Stripe Card Payments appears, and on US stores, your sales tax setting.
4. Switch outside a sale period and place test orders with each card type and wallet.
5. Keep the old account open for refunds and disputes on earlier orders.
6. Compare the first full month of fees against your estimate.

If you want PayPal in the mix as well, my Shopify Payments vs PayPal comparison explains how that fits.

Frequently asked questions

Sources

1. Stripe pricing (US), Stripe
2. Stripe pricing (UK), Stripe
3. Update Shopify payment provider to Stripe Card Payments, Stripe Support
4. Shopify customer story, Stripe
5. Using Shopify Payments with a third-party provider, Shopify Help Center
6. Payments apps, Shopify Developer Docs

Related services and work

Written by Ashraf Siddik

I'm a Shopify developer and CRO specialist. I have built and improved Shopify stores since 2018, completed more than 1,000 projects, and hold a 4.96 average rating across 719 client reviews.

About me · Client reviews