Shopify Payments vs Stripe for DTC Brands: Fees, Subscriptions, and Who Controls Your Payments

Every few weeks a founder asks me the same question: "Should we be on Shopify Payments or Stripe?" It sounds like a choice between two processors. For a brand selling on Shopify in the US, it usually isn't. Shopify Payments is Shopify's own payment service, supported in part by Shopify's agreement with Stripe. Your own Stripe account normally doesn't appear at all in a US Shopify checkout.

So the useful question is different: who do you want your payment relationship to be with, and on which checkout? You can let Shopify run payments inside its checkout. You can bring a third-party gateway into Shopify and pay Shopify an extra fee for it. Or you can run part of your sales, often funnels, landing-page checkouts or subscriptions, through your own Stripe account outside Shopify's checkout.

This guide compares those setups on the things that move margin and risk for DTC brands: fees at real volume, payouts and holds, dispute costs, subscription support, and whether your saved customer cards can come with you if you ever need to move.

Key takeaways

• On a US Shopify store, Stripe is usually not offered as a separate card gateway. Shopify Payments is the default, and Shopify's own filings say its Stripe and PayPal agreements support it.
• Shopify Payments costs 2.9% + 30¢ on Basic, falling to 2.5% + 30¢ on Advanced and from 2.25% + 30¢ on Plus. Stripe's standard online rate is 2.9% + 30¢ (US list prices, October 2026).
• The expensive mistake is a third-party gateway inside Shopify's checkout: Shopify adds 0.2% to 2% per transaction on top of the gateway's own fee. At $100,000 a month on the Grow plan, that is $1,000 extra.
• Both charge a $15 dispute fee in the US, but Shopify returns it when you win. Stripe keeps the $15 and adds a $15 fee for countering, which it refunds only if you win.
• Stripe will export stored cards to another PCI DSS Level 1 processor. Shopify documents how to import cards but not how to export them. That matters most to subscription brands.

Shopify Payments vs Stripe at a glance

Rates are the published US list prices on Shopify's pricing page and Stripe's pricing page as of October 2026. Plan subscription fees are not included.

On Shopify, you rarely choose Stripe directly

Most comparison articles skip this. Shopify's FY2025 annual report says Shopify has payment service provider agreements with Stripe and PayPal that directly support Shopify Payments. When you activate Shopify Payments, you sign up, get paid and handle disputes inside Shopify. Any Stripe infrastructure underneath runs under Shopify's agreement, not under a Stripe account of your own.

Because of that, Shopify generally doesn't offer Stripe as a separate card gateway in countries where Shopify Payments is available. A Shopify reply on the Community forum put it directly: "By default Stripe isn't an option in regions that are supported by Shopify Payments." The same reply says Shopify's payments team can switch Shopify Payments off for stores selling products Shopify Payments doesn't support, so those stores can keep using Stripe. Where Stripe is available inside Shopify, it now runs through the newer Stripe Card Payments provider, which Stripe says supports Shopify Subscriptions and third-party subscription apps as of June 1, 2025.

In practice, DTC brands end up in one of three setups, sometimes more than one at once:

1. Shopify checkout + Shopify Payments. The default. One account, one dashboard, no extra transaction fee.
2. Shopify checkout + a third-party gateway. Usually a brand that Shopify Payments won't support, or one with an existing merchant account it wants to keep. Shopify charges its third-party transaction fee on every order.
3. Your own checkout + your own Stripe account. Funnels, landing-page checkouts, post-purchase upsell flows and subscription billing that run outside Shopify's checkout. Shopify's transaction fee doesn't apply because the payment never goes through Shopify checkout.

Fees: what each setup costs at $100,000 a month

Take a brand with $100,000 a month in US domestic online card sales and a $60 average order, which works out to about 1,667 orders. The 30¢ fixed fee adds about $500 a month in every setup. The percentage is what changes.

Three things stand out.

Inside Shopify checkout, Shopify Payments usually wins on cost. On Grow, the card rate is 0.2 points below Stripe's list price, and there's no third-party fee. On Advanced and Plus the gap widens.

A third-party gateway inside Shopify only makes sense for a reason other than price. Even if your gateway matched Shopify's rate, Shopify's fee (2% on Basic, 1% on Grow, 0.6% on Advanced, 0.2% on Plus) would still apply. Brands accept it when Shopify Payments isn't available to them, or when they need a dedicated merchant account for their category.

Stripe's list price is a starting point. Stripe offers custom pricing to larger businesses, and your own checkout carries its own costs: the checkout or funnel software, subscription billing, and the work of running it. Compare the total cost, not only the card rate.

Payouts and account holds

Stripe typically schedules your first payout 7 to 14 days after the first live payment, depending on industry, country and risk level. After that, US accounts settle on a standard T+2 schedule. Shopify Payments lets you choose daily, weekly or monthly payouts, with timing set by country.

Both can hold funds. Shopify Payments applies reserves "to cover potential disputes and refunds", and Stripe can delay payouts or add reserves when it sees risk. Both are aggregators, so the risk decisions follow their platform-wide policies rather than an underwriting file built for your business.

The difference is what an account problem stops. If Shopify Payments restricts or closes your account, card acceptance on your Shopify checkout stops with it, and your store is still on Shopify. We covered that scenario in our Shopify account termination recovery guide. A separate Stripe account doesn't share that dependency, but on its own it's still a single point of failure for whatever runs through it.

Disputes: same fee, different refund rules

Both charge $15 per dispute in the US. The refund rules differ:

• Shopify Payments: $15 per chargeback, and "if you win the chargeback, then the fee is returned to you."
• Stripe: $15 dispute received fee, which is never returned unless your contract says otherwise. Since June 17, 2025, countering a dispute adds a $15 dispute countered fee, refunded only if you win.

At low volume this barely matters. It matters once disputes become routine. Say you get 40 disputes a month, counter every one, and win 30% (12 cases). On Shopify Payments you pay $600 and get $180 back, so $420 net. On Stripe you pay $600 in received fees plus $600 in countered fees and get $180 back, so $1,020 net. With Stripe, it pays to counter only the disputes you can win.

Subscriptions: where renewals are allowed to run

For subscription brands this section matters more than the rate table.

Inside Shopify, subscription apps can only charge renewals through gateways Shopify supports for subscriptions. As of October 2026, Shopify's help center lists Shopify Payments, PayPal Express, Authorize.net, Adyen (only for businesses with an existing Adyen approval) and Stripe ("available only to select merchants"). There are limits even within that list. With Shopify Payments, some stores can offer only Shop Pay for subscriptions, and Apple Pay subscriptions are limited to Visa and Mastercard.

With your own Stripe account, renewals run wherever your billing system runs: Stripe Billing at 0.7% of billing volume on pay-as-you-go, or a subscription platform that connects to Stripe. You control the retry schedule, the dunning emails and the customer portal. You also take on the work of running them well. If you plan to bill renewals across more than one gateway, our guide to recurring billing across multiple payment gateways covers stored credentials, routing and duplicate-charge prevention.

Card portability: can your subscribers move with you?

A one-time buyer can re-enter a card at checkout next time. A subscriber who has to re-enter a card because you changed provider is a churn risk. So find out who holds the stored cards before you build a large recurring base on them.

Stripe says the businesses using it own the card data they store there. If you leave, Stripe will send an encrypted export of stored cards to another PCI DSS Level 1-compliant processor. Credentials saved through Link are excluded.

Shopify documents how to bring cards in: subscription contracts from Stripe, Braintree, PayPal Express and Authorize.net can be migrated into Shopify, and Shopify Professional Services can import card numbers for Plus and Enterprise stores. Its help center doesn't describe a way to export stored payment methods out. When a brand asked in 2022, Shopify staff said there was "currently no possible way of exporting that data to a new gateway" and that customers would need to re-submit their payment details. Check the current position with Shopify before you rely on moving a subscriber base later.

Category rules: both keep a restricted list

Neither option fixes a category problem. Stripe's restricted businesses list prohibits negative option marketing and reduced-price trials with unclear or hidden pricing. It treats CBD products with only negligible THC, and e-cigarettes sold in line with the law, as restricted, which means extra review. Shopify has its own rules, and some categories can't sell on Shopify at all, as vape brands found out (see can you sell vapes on Shopify in 2026). If your products sit near either list, plan for a dedicated merchant account underwritten for your business rather than counting on an aggregator to approve you.

Which one fits your brand?

Where Paysight fits

Paysight isn't a payment processor, and it doesn't replace Shopify Payments or Stripe. It's a platform for launching and managing subscriptions on the gateways and merchant accounts you connect yourself, such as Stripe, NMI, Finix or your own MIDs. Each gateway still makes its own underwriting decision, so Paysight doesn't make a restricted product acceptable.

For brands that run checkout or recurring billing on their own gateways, Paysight keeps subscription, transaction and customer data in one place. It routes and retries payments across the gateways you've connected, keeps stored cards current with a card account updater, and gives customers care portals to manage their subscriptions. For Shopify stores, the Paysight Shopify dashboard brings storefront data together with checkout and payment data, so you can follow a customer from visit to purchase.

Sources

• Shopify pricing: plan card rates, international rates and third-party transaction fees (accessed October 2026)
• Stripe pricing: card rates, dispute fee, Stripe Billing (accessed October 2026)
• Shopify Inc. Form 10-K for fiscal 2025: payment service provider agreements with Stripe and PayPal
• Shopify Community: using an existing Stripe account on a US Shopify store (October 2021)
• Stripe Support: moving Shopify stores to the Stripe Card Payments provider
• Shopify Help Center: third-party payment providers and transaction fees
• Shopify Help Center: chargeback fees by country
• Stripe Docs: how disputes work and dispute fees
• Stripe Support: June 2025 pricing updates for disputes
• Stripe Docs: payouts and settlement timing
• Shopify Help Center: Shopify Payments payouts and reserves
• Shopify Help Center: subscriptions considerations and supported payment gateways (accessed October 2026)
• Shopify Help Center: migrating subscription payment methods
• Shopify Community: transferring customer payment data off Shopify Payments (July 2022)
• Stripe Docs: request a payment data export
• Stripe: prohibited and restricted businesses (accessed October 2026)