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Stripe vs Shopify Payments: Ultimate Comparison 2026

John Ahya
Written by John Ahya
Updated on
date March 12, 2026
Category Shopify

Stripe vs. Shopify

When running an online business or a store, you need to decide on many things. Out of these, the payment processor is one of the most crucial things.

Why?

Because customers want a reliable, secure, convenient, and super-fast payment experience. Hence, it would help if you first understood the importance of payment processors.

By offering a streamlined payment experience to your customers by integrating popular payment processors, you gain the customers’ trust in the first instance. On the other hand, a bad payment gateway can result in delayed, lost, or failed transactions, drawing customers away from your business. Therefore, integrating a reliable payment processor is not only necessary for customers but also a crucial part of business strategy.

If you are running your online business on Shopify, it has a built-in payment processor known as Shopify Payments, which integrates perfectly with the online store.

Besides this, you also have an option to integrate a third-party payment processor into your website. For the same, you can choose a leading payment processor, such as Stripe.

Now, you might have a question, whether to leverage Shopify Payments or Stripe? How is the built-in payment gateway different from Stripe?

To simplify your task, we will compare Stripe vs Shopify Payments based on some essential factors.

So, let’s dive right in.

A Brief Overview of Stripe and Shopify Payments

Whenever you look for a payment processing platform, there is a high possibility you will come across Stripe and Shopify Payments. Even though both are the leading online payment processing platforms, they serve businesses in a much different manner.

Stripe is one of the fastest-growing standalone payment processing platforms that power both in-person and online payments. It supports many payment methods and currencies, which makes it the go-to solution for businesses of all sizes, whether they operate locally or globally.

Shopify Payments is a built-in payment processor that allows you to accept payments via multiple methods in a streamlined manner. However, it primarily works with the eCommerce stores built on the Shopify platform. It is quick to set up and allows management to make payments from the Shopify dashboard.

Here, we will compare Stripe vs Shopify Payments based on essential factors to help you choose the best for your business. However, we will quickly compare these payment processors.

Stripe vs Shopify Payments: A Quick Comparison

Let’s quickly go through a simple yet effective comparison of Stripe vs Shopify Payments before diving deep into it.

Factors Stripe Shopify Payments
Transaction Fees 2.9% + 30 cents 2.5% – 2.9% + 30 cents
Implementation Integrated into stores and other software to make seamless payments Standalone software with POS and online payment processing abilities
Invoicing / Billing 0.4%–0.5%; 0.5%–0.8% recurring Invoicing comes free; Recurring billing needs a subscription app from its official Shopify App Store
International Fees 1% for cross-border transactions. Extra 1% currency conversion fee. Sending money requires paying a mid-market currency conversion fee. 1.5% to get paid in the US.
Countries Available Available across 46 countries Available in 38 countries
Best Use Cases Best of recurring online payments, especially best for B2B markets Best for small retailers and online stores

Stripe Vs Shopify Payments: Key Differences to Be Discussed

Here, we will compare Stripe vs Shopify Payments based on the key factors to help you choose the best for your business.

Ease of Use And Integration to Store

Stripe:
Stripe is known for its flexibility and robust set of features, catering to businesses of all sizes. While its integration process might require a bit more technical know-how compared to Shopify Payments, Stripe offers comprehensive documentation and developer tools to facilitate smooth integration.

Shopify Payments:
Shopify Payments is an inherent part of Shopify’s ecosystem, offering a straightforward setup process for merchants. With its user-friendly interface and step-by-step guidance, even beginners can easily navigate through the integration process.

Additionally, Shopify Payments is ideal for businesses that prefer not to rely on third-party payment processors. By using it, merchants can simplify the entire checkout process and reduce the need for extra integrations or external accounts. This built-in solution helps streamline payment management, allowing store owners to handle everything directly from their Shopify dashboard without juggling multiple platforms.

Winner: Shopify Payments emerges as the clear winner for its seamless integration process, user-friendly interface, and dedicated support resources.

Equipment Needed for Offline Payments

Stripe:
Stripe enables in-person payments through compatible card readers and point-of-sale (POS) hardware. Merchants typically need devices such as the BBPOS WisePOS E or Verifone P400, which integrate directly with Stripe’s payment infrastructure. These card readers support tap, chip, and swipe payments and connect easily with Stripe’s software for seamless transaction processing.

Depending on the features such as wireless connectivity, touchscreen displays, or receipt printing, hardware costs generally range from around $59 to $299.

Shopify Payments:
Shopify Payments also requires merchants to use Shopify-approved card readers for accepting offline transactions. Shopify provides a range of hardware options to work smoothly with its POS system, including tap-and-chip card readers and more advanced retail setups. These devices are available directly through Shopify and are designed for easy setup and integration with Shopify stores.

Pricing typically starts at around $59 for basic readers, with more advanced POS hardware available for businesses needing additional functionality.

Winner: Both Stripe and Shopify Payments offer reliable hardware options for in-person payments, with similar pricing and functionality. As a result, this category ends in a tie, since merchants will need to purchase compatible card readers regardless of the platform they choose.

Struggling to Decide Between Stripe and Shopify
Payments?

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Pricing and Transaction Fees

Stripe:
Stripe charges transaction fees according to the type of payment; it does not charge a subscription fee. There is a 2.9% plus $0.30 fee for debit and credit card payments made online and a 2.7% plus $0.05 fee for in-person transactions. Payments with foreign cards, local payment options, ACH credit and debit, and online invoicing software for small businesses are subject to additional fees.

Shopify Payments:
If you choose Shopify as your eCommerce platform for your store, you can integrate Shopify Payments, an inherent payment gateway. The primary benefit of leveraging Shopify Payments is that it offers free setup, cancellation, PCI compliance, and more.

There will be no transaction fees whenever you leverage Shopify Payments as your go-to solution.

However, if you don’t use Shopify Payments as your default payment method, you have to pay specific transaction fees.

By using Shopify payments, you only need to pay the card rates depending on your Shopify plan. They are as follows.

  • Basic: 2.9% + $0.30 for every online payment and 2.6% + $0.10 for every in-person transaction.
  • Grow: 2.7% + $0.30 per every transaction online and 2.5% + $0.10 for each in-person transaction.
  • Advanced: 2.5% + $0.30 for every online and 2.4% + $0.10 in-person transaction.
  • Shopify Plus: Transaction fees vary depending on your customized plan.

Please note that Shopify Plus charges a 1% additional fee for every international transaction. From the above payment processing fees, it’s clear that the higher the plan, the lower the card transaction fees.

Winner: Here, both Stipe and Shopify payments provide competitive pricing. However, Shopify Payments leads the race due to its cost-effectiveness. When you opt for the Shopify Payments available within Shopify, you bypass the transaction fees. Hence, it becomes an inexpensive option compared to Stripe.

Payout Time

Stripe:
Stripe offers a couple of days payout time for most transactions. It means that the amount received from a customer’s purchase is usually transferred into your account within two business days. If you are one of those eCommerce entrepreneurs who always prefer faster payouts, Stripe is an amazing option to opt for, as it helps you maintain a healthy cash flow.

Shopify Payments:
Any payments made to your account using Shopify Payments on Fridays, Saturdays, and Sundays (UTC) will be processed as a single payment. You can take money out of Shopify Balance in a single business day. If consumers use Shop Pay installments at checkout, they will get their money in three business days.

Winner: Stripe is ahead in the race in payout time as it offers you more control over your funds.

Available Countries

Countries Available Source: Shopify

Stripe:
As discussed in the above table, Stripe is available in 46 countries, including major markets such as the USA, UK, Canada, and Australia. It keeps expanding its reach, allowing online store owners to accept payments worldwide. This broad availability makes Stripe the best option for stores with global customers or those looking to enter the new market.

Shopify Payments:
Compared to Stripe, Shopify Payments operates across 38 countries. Even though it serves many vital markets, it might still need to be active in some areas. Despite its limited breadth, Shopify Payments improves the user checkout experience by providing localized payment methods in supported countries.

Winner: Stripe wins in this comparison because who does not like to integrate a payment processor that is accepted globally?

Fraud Protection

Stripe:
Stripe offers advanced fraud protection features to help merchants safeguard their transactions against fraudulent activities. These features include customizable fraud detection rules, which allow merchants to set specific parameters to identify suspicious transactions based on their unique business needs.

Shopify Payments:
Shopify Payments offers built-in fraud protection tools to help merchants detect and prevent fraudulent transactions. These tools include address verification and CVV checks, which help verify the authenticity of each transaction and reduce the risk of fraudulent activities — a crucial safeguard considering how fraud and payment issues remain among the common challenges faced by eCommerce businesses.

Winner: It’s Tie. Both Shopify Payments and Stripe offer robust fraud protection measures to help merchants mitigate the risk of fraudulent transactions.

Accepted Payment Methods

If you are going to utilize Stripe or Shopify Payments for your business, it’s essential that you are familiar with their payment methods.

Stripe:
Stripe is a global payment platform, available in 46 countries, and it is well-known for its versatility. It accepts payments via different methods, as follows.

  • Credit and debit cards are available through leading networks such as Visa, MasterCard, and American Express.
  • Checkout easily using different wallet payment methods, such as AliPay, Google Pay, Amazon Pay, Apple Pay, etc.
  • Make payments via bank debits or transfers, such as ACH Credit Transfer, ACH Direct Transfer, and more.
  • Accept payments via BNPL, cash-based vouchers, real-time payments, cryptocurrencies, and more.

Shopify Payments:
Shopify Payments provides services in over 38 countries and accepts payments in 130 currencies. Despite there is some variation based on the location, it accepts payments using the following methods:

  • Debit and Credit Cards from Mastercard, Visa, and more.
  • Digital wallets such as Facebook Pay, Apple Pay, Google Pay, etc.
  • Multiple local and international payment methods.
  • PayPal
  • Popular manual payment methods.

Although Shopify accepts various payment methods, it doesn’t accept some international methods, such as cryptocurrencies. Hence, it could be challenging for businesses that want to expand globally.

Winner: Stripe leads the race when we talk about payment options because of its worldwide reach, along with a range of methods, such as cryptocurrency, digital wallets, and banks.

Dispute and Chargeback Fees

Stripe:
Stripe charges a $15 fee for each disputed transaction (chargeback). If the case is settled in your favor, you will receive your money back. Additionally, if there are a lot of chargebacks or fraudulent activities, Stripe can charge more. Chargeback costs can hurt a company’s earnings, but Stipe’s refund policy encourages merchants to resolve disputes and reduce chargeback incidents proactively.

Shopify Payments:
Like Stripe, Shopify Payments likewise costs a $15 fee for each disputed transaction (chargeback). Similar to Stripe, this cost could be reimbursed if the merchant wins the dispute. On the other hand, excessive chargebacks or fraudulent conduct could result in higher fees.

Shopify Payments encourages merchants to adopt efficient risk management techniques and uphold a high standard of customer satisfaction to minimize chargebacks by imposing consistent fines for disputes.

Winner: Stripe is the winner because the platform has launched a new Stripe Radar feature that helps merchants prevent fraudulent activities.

Stripe vs Shopify Payments: Advantages and Disadvantages

Before choosing between Stripe and Shopify Payments, it helps to look at their overall strengths and limitations. While both platforms offer reliable payment processing, they differ in terms of flexibility, ease of use, and ecosystem integration. Understanding these advantages and disadvantages can help merchants decide which solution better fits their business needs.

Stripe Advantages

  • Highly customizable payment infrastructure: Stripe offers powerful APIs and developer tools that allow businesses to build custom checkout experiences and payment workflows.
  • Supports global payments: Stripe works in many countries and supports multiple currencies and international payment methods.
  • Advanced features for complex businesses: It provides tools for subscriptions, recurring billing, marketplaces, and SaaS platforms.
  • Flexible integrations: Stripe can integrate with many eCommerce platforms, mobile apps, and custom-built websites.

Stripe Disadvantages

  • Requires more technical setup: Businesses without technical knowledge may find Stripe harder to configure compared to built-in solutions.
  • Not a native solution for Shopify stores: Shopify merchants may face additional transaction fees if they use Stripe instead of Shopify Payments.
  • Hardware and integrations may require extra configuration: Setting up POS systems or custom integrations can take more time.

Shopify Payments Advantages

  • Seamless integration with Shopify: Since it is Shopify’s built-in payment gateway, it works directly with the platform without requiring third-party setup.
  • Simple and beginner-friendly: Merchants can activate Shopify Payments quickly and manage transactions from the Shopify dashboard.
  • No additional Shopify transaction fees: Using Shopify Payments helps merchants avoid extra fees charged for third-party payment gateways.
  • Integrated reporting and order management: Payments, orders, and analytics are managed in one unified system.

Shopify Payments Disadvantages

  • Limited to Shopify stores: Businesses that operate outside the Shopify ecosystem cannot use Shopify Payments independently.
  • Available in fewer countries than Stripe: Shopify Payments is supported in a limited number of regions compared to Stripe.
  • Less flexibility for custom payment setups: Merchants who need advanced customization or complex payment workflows may find it restrictive.

Overall, both Stripe and Shopify Payments offer strong payment processing capabilities, but the best option depends on your business structure, platform preference, and technical requirements.

Stripe or Shopify Payments: Which One Should You Choose?

Both Stripe and Shopify Payments are reliable options for processing online payments. The right choice mainly depends on how your business operates and what level of flexibility you need. While Shopify Payments is built specifically for Shopify stores and keeps things simple, Stripe works as a more flexible standalone payment processor that can be customized for different types of businesses.

Here’s a quick way to decide which one may suit your needs better.

When to Choose Stripe

Stripe is a good option if your business needs more control over how payments work. It’s widely used by companies that require custom payment setups or operate beyond a single online store.

Stripe may be the better choice if:

  • You run a marketplace or multi-vendor platform. Stripe can handle complex payment flows, such as splitting payments between multiple sellers.
  • Your business needs custom payment integrations. Stripe offers powerful developer tools and APIs that allow businesses to build tailored checkout experiences.
  • You sell internationally. Stripe supports multiple currencies and a wide range of global payment methods.
  • Your business model includes subscriptions or recurring billing. Stripe provides strong tools for managing subscription payments and automated billing.

When to Choose Shopify Payments

Shopify Payments works best for merchants who already run their store on Shopify. Since it’s built directly into the platform, it removes the need for third-party payment integrations and keeps everything in one place.

Shopify Payments may be the better option if:

  • You run a Shopify store. The setup is quick and doesn’t require additional integrations.
  • You want a simple payment setup. Everything from checkout to payment tracking can be managed inside the Shopify dashboard.
  • You want to avoid extra transaction fees. Shopify typically charges additional fees when third-party gateways are used, which you can avoid with Shopify Payments.
  • You prefer an all-in-one eCommerce solution. Shopify Payments works seamlessly with Shopify’s checkout, orders, and reporting tools.

The Final Verdict

In short, choosing between Stripe and Shopify Payments boils down to your business’s requirements. Both offer a faster checkout experience and robust features, but Stripe shines regarding global reach and customization options. Whichever option you choose—a simplified payment process integrated into your eCommerce platform or flexibility and customization up top—both offer competitive dispute resolution solutions and dependable support.

The choice ultimately comes down to your preferences, business plan, and desired growth rate. Thus, thoroughly consider your options and select the payment option that propels your eCommerce store forward with scalability options.

Still feeling torn between Stripe and Shopify Payments? Don’t worry, WebDesk Solution is here to simplify your payment journey. We offer eCommerce development services and we have expertise in integrating payment gateways into online stores.

John Ahya

John is the President and Co-Founder of WebDesk Solution, a leading eCommerce development company. With extensive expertise across all major eCommerce platforms, he continually explores the dynamic world of online commerce. A nature enthusiast, John enjoys recharging amidst the fresh mountain air during his vacations.

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