No — but they’re closely related. Shopify Payments is built on top of Stripe’s infrastructure. When a customer pays through your Shopify store using Shopify Payments, Stripe processes that transaction behind the scenes. But Shopify Payments is not Stripe. It’s Shopify’s own product with its own pricing, its own rules, and its own limitations.
Stripe doesn’t own Shopify. They’re separate companies. Shopify licensed Stripe’s technology to power its built-in payment processing. Think of it like this: Stripe is the engine, Shopify Payments is the car.
What’s the Difference Between Stripe and Shopify Payments?
Shopify Payments only works on Shopify. It’s locked to the Shopify ecosystem. You can’t use Shopify Payments on a WooCommerce site, a custom website, or any other platform. Stripe works everywhere.
Shopify Payments eliminates the third-party transaction fee. If you use Stripe directly (or any other external gateway) on Shopify, Shopify charges you an additional 0.5–2% per transaction on top of your processing fees. Using Shopify Payments avoids that. This is the #1 reason most Shopify merchants use Shopify Payments instead of connecting Stripe directly.
Different dashboards and controls. Shopify Payments is managed inside your Shopify admin. Stripe is managed in Stripe’s separate dashboard. Shopify Payments gives you less control over fraud settings, retry logic, and payment configuration than Stripe’s dashboard does.
Same restrictions, different enforcement. Both restrict the same types of businesses — but Shopify goes further. If Shopify flags your business as prohibited, you lose both your payment processing AND your storefront simultaneously. With Stripe alone, only the payment side is affected.
Can I Use Stripe Instead of Shopify Payments?
Yes. Shopify lets you connect Stripe (or dozens of other payment gateways) as an external provider. The trade-off: Shopify charges a transaction fee of 0.5–2% on top of whatever your external gateway charges.
For most standard Shopify merchants, this makes Shopify Payments the obvious choice. But if you need features Shopify Payments doesn’t offer — like multi-MID routing, cascading, or a dedicated payment gateway — connecting an external processor through Shopify and absorbing the extra fee may be worth it. Especially if your business is in a restricted category where Shopify Payments will eventually shut you down anyway.
Which Has Lower Fees — Stripe or Shopify Payments? is Stripe?
On paper, similar. Shopify Payments charges 2.4–2.9% + $0.30 depending on your Shopify plan. Stripe charges 2.9% + $0.30 on its standard US pricing.
The real difference is the third-party fee. Using Stripe on Shopify means you pay Stripe’s rate PLUS Shopify’s 0.5–2% surcharge. Using Shopify Payments means you only pay one rate.
But neither gives you interchange-plus pricing, which is almost always cheaper at scale. Both are payment aggregators using flat-rate pricing. If you’re processing $25K+/month on Shopify, a dedicated merchant account with interchange-plus rates through an external gateway will likely save you money — even with Shopify’s surcharge. See our Stripe fees breakdown for the full picture.
Does Shopify Payments Offer Anything Stripe Doesn’t?
Yes — a few Shopify ecosystem features that only work with Shopify Payments:
Shop Pay. Accelerated checkout for returning customers. Saves their shipping and payment details for one-tap purchasing. Only available through Shopify Payments.
Shopify Capital. Business loans and cash advances based on your sales history. Only available to Shopify Payments users.
No third-party transaction fee. The 0.5–2% surcharge only applies to external gateways. Shopify Payments users don’t pay it.
On the flip side, Stripe offers more developer flexibility, works with any platform, supports more countries and currencies, and gives you more granular control over fraud tools and payment configuration.
Can High-Risk Merchants Use Either One?
Not reliably. Both Stripe and Shopify Payments are payment aggregators with automated risk systems that freeze accounts without warning. If your business is in supplements, coaching, travel, subscriptions with high churn, or any category on their restricted list — it’s a matter of when they shut you down, not if.
The safer setup: use Shopify as your storefront but connect a dedicated merchant account through an external gateway. You lose the third-party fee benefit but gain stability, interchange-plus pricing, and a processor that won’t pull the plug on your entire business because their algorithm flagged a volume spike.
Stripe vs. Shopify Payments: Which One is Right for You?
Choosing between Stripe and Shopify Payments—whether you frame it as Shopify vs Stripe or Stripe vs Shopify—depends largely on your business’s specific needs and the eCommerce platform you’re using. Here’s a general guide to help you decide.
Choose Stripe If:
- Customization is Key: Stripe’s robust APIs make it highly customizable, offering flexibility that can be vital for unique business models. If you have specific requirements for your payment process and have the technical resources to implement them, opening a Stripe account is a compelling choice.
- You Operate Internationally: Stripe operates in more countries (46 vs. 33+) and supports more currencies than Shopify Payments. If you’re looking to cater to a diverse, global customer base, Stripe may be the more fitting option.
- You’re Not on Shopify: If you’re using an eCommerce platform other than Shopify, or if you’re not running an eCommerce business, Stripe’s compatibility with a wide range of platforms and apps makes it a versatile choice.
Choose Shopify Payments If:
- You Use Shopify: If your business is already using or planning to use a Shopify account as its eCommerce platform, Shopify Payments offers seamless integration, simplifying your payment process.
- You Prefer an All-in-One Solution: Shopify Payments is tightly integrated with other Shopify services, providing a holistic solution for your eCommerce needs.
- You Want to Avoid Extra Transaction Fees: When using Shopify Payments, you avoid the additional transaction fees (0.6%–2%) that Shopify charges when using other payment gateways.
- You Want 24/7 Phone and Chat Support: Shopify Payments, through Shopify’s support channels, offers round-the-clock phone and chat support.
Common Questions
No. Stripe and Shopify are completely separate companies. Shopify licenses Stripe’s payment infrastructure to power Shopify Payments, but there’s no ownership relationship.
Not exactly. Shopify Payments uses Stripe’s technology under the hood, but it’s Shopify’s product with its own pricing, policies, dashboard, and features like Shop Pay and Shopify Capital that Stripe doesn’t offer.
Both charge $15 per chargeback and use similar dispute processes since Shopify Payments runs on Stripe’s infrastructure. The critical difference: if Shopify suspends your store for policy violations, you lose your storefront AND your payment processing at the same time. With Stripe alone, only the payment side goes down.
For most standard Shopify merchants: use Shopify Payments. The third-party fee savings and Shop Pay make it the simpler choice. For high-risk merchants or businesses processing $25K+/month that want interchange-plus pricing and more control: connect an external gateway and accept the surcharge.
Mostly. Both support major credit and debit cards, Apple Pay, Google Pay, and local payment methods. Shopify Payments also supports Shop Pay. Stripe supports a wider range of international payment methods and currencies.
Shopify Payments is available in 23 countries. Stripe is available in 47+. If you’re selling from a country Shopify Payments doesn’t support, Stripe or another external gateway is your only option.
The Bottom Line
If you’re on Shopify and you’re low-risk, Shopify Payments is the path of least resistance. If you’re high-risk, scaling past $25K/month, or need processing redundancy — a dedicated merchant account through an external gateway is the smarter play, even with Shopify’s surcharge. DirectPayNet helps Shopify merchants set up the right payment infrastructure for their situation. Let’s talk.
