Shopify Payments vs Stripe: 7 Key Differences to Know

Did you know that 70% of online shoppers abandon their carts due to unexpected fees or limited payment options? 

Choosing the right payment processor is critical for merchants looking to reduce friction, improve conversions, and minimize transaction costs. 

Shopify Payments and Stripe are two of the most popular choices, but they cater to different business needs.

Whether you're a Shopify-exclusive seller looking for a seamless, built-in solution or a multi-platform business in need of greater flexibility, understanding their differences is key. 

Our guide breaks down the seven critical factors that set these platforms apart, helping you make an informed decision that aligns with your business model.

Quick overview of Shopify Payments vs Stripe

Both Shopify Payments and Stripe offer reliable payment processing solutions, but their key differences lie in integration, customization, fees, and fraud prevention. 

Below is a quick comparison to help merchants choose the best option for their business.

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For Shopify-based businesses, Shopify Payments offers a cost-effective, plug-and-play solution. However, for those needing custom payment flows, multi-platform support, or advanced fraud protection, Stripe is the better choice.

7 Key Differences between Shopify Payments and Stripe

While both payment processors facilitate online transactions, they differ significantly in features, flexibility, and overall functionality. ChargePay has highlighted seven key concerns that seller must know.

Customization

Shopify Payments is a built-in payment processor designed for Shopify stores, limiting customization to Shopify’s ecosystem. 

It offers seamless integration but provides fewer options for modifying checkout flows, branding, and payment processing logic. 

Customization is primarily restricted to Shopify’s default checkout settings and third-party apps available in the Shopify App Store.

Stripe, on the other hand, is a developer-centric payment processor offering extensive customization options. 

Merchants can tailor the entire payment experience using Stripe’s APIs, allowing modifications in payment flows, checkout design, and risk assessment. 

Businesses with unique payment needs—such as multi-currency processing, dynamic payment routing, or custom fraud detection—can leverage Stripe’s flexibility to optimize transactions.

In short, Shopify Payments is ideal for those seeking a streamlined, Shopify-native experience, while Stripe provides advanced customization capabilities for businesses requiring greater control over their payment infrastructure.

Payout time

Shopify Payments typically processes payouts within 2 to 3 business days for U.S. merchants, though this vary based on country and risk factors. Transactions made on weekends or holidays may experience slight delays. 

Since Shopify Payments is directly integrated with Shopify, merchants benefit from automatic payouts without needing manual withdrawals.

Stripe, on the other hand, has a standard payout time of 2 business days for U.S. merchants, with faster options available for eligible businesses. 

High-risk accounts or international transactions may experience longer wait times, sometimes up to 7 business days, depending on Stripe’s risk assessment. 

Stripe also provides instant payouts for an additional fee, allowing merchants to access funds immediately.

While both platforms offer reliable payout schedules, Shopify Payments ensures direct deposit automation within Shopify’s ecosystem, whereas Stripe provides more flexibility, including instant payouts for urgent cash flow needs.

Chargebacks

Chargebacks are a shared challenge for businesses using Shopify Payments and Stripe. 

When a customer disputes a transaction, both platforms automatically deduct the disputed amount from the merchant’s balance until the case is resolved. 

Chargeback fees also apply—Shopify Payments typically charges $15 per chargeback for U.S. merchants, while Stripe imposes a $15 dispute fee, refunded if the dispute is won.

Both platforms provide merchants with tools to respond to disputes, including dispute dashboards, evidence submission, and fraud prevention settings. 

However, neither eliminates chargeback risks entirely, making proactive chargeback management essential.

ChargePay integrates with both Shopify Payments and Stripe to help businesses prevent, manage, and win chargeback disputes. 

With AI-driven fraud detection, predictive analytics, and automated dispute resolution, ChargePay reduces chargeback occurrences and increases win rates.

Worldwide Availability

Shopify Payments is available in 23+ countries, including the U.S., Canada, the U.K., Australia, and major European regions. 

However, it is not accessible in high-risk regions or countries with strict financial regulations. 

Merchants outside supported locations must rely on third-party gateways, such as Stripe or PayPal, to process payments on Shopify.

Stripe, in contrast, operates in over 45+ countries and supports a broader global reach, including parts of Asia, Latin America, and emerging markets. 

Stripe also supports 135+ currencies, allowing businesses to process payments from international customers without conversion complications. 

Additionally, Stripe enables local payment methods, such as SEPA for Europe and Alipay for China, making it a preferred choice for global expansion.

For merchants operating internationally, Stripe offers greater coverage, while Shopify Payments provides a more streamlined experience for those within its supported regions.

Integration

Shopify Payments is a fully integrated payment solution within the Shopify ecosystem. Merchants using Shopify can enable it with a single click, eliminating the need for third-party payment gateways. 

Transactions, refunds, and chargebacks sync seamlessly with Shopify’s analytics, reducing the complexity of payment reconciliation. 

However, Shopify Payments is exclusive to Shopify stores, meaning businesses cannot use it on external platforms.

Stripe, in contrast, is a standalone payment processor that integrates with thousands of platforms, including Shopify, WooCommerce, Magento, and custom-built websites. 

It provides a developer-friendly API, allowing businesses to create custom checkout flows, automate invoicing, and manage payments across multiple channels. 

Stripe also supports advanced payment features like subscription billing, on-demand payouts, and embedded payments, making it a more flexible choice for businesses operating beyond Shopify.

For Shopify-exclusive businesses, Shopify Payments offers a frictionless experience. 

However, merchants needing a multi-platform payment processor with customization options may find Stripe’s integration capabilities more suitable.

Fraud Filter & protection

Shopify Payments includes basic fraud protection features, such as automatic risk analysis, CVV verification, and AVS. 

It also provides Shopify’s built-in fraud analysis tool, which flags high-risk orders based on transaction data, helping merchants reduce fraud-related chargebacks. 

However, Shopify Payments does not offer advanced fraud prevention customization beyond Shopify’s ecosystem.

Stripe, on the other hand, offers a more robust fraud prevention suite through Stripe Radar, an AI-powered tool that analyzes payment risk in real-time. 

Stripe Radar uses machine learning algorithms trained on billions of transactions to detect fraudulent behavior, automatically blocking high-risk payments. 

Businesses can customize fraud detection settings, implement risk scoring models, and set manual review triggers for suspicious transactions.

For basic fraud protection, Shopify Payments is sufficient. However, businesses needing advanced fraud detection with AI-driven insights and customizable risk controls may benefit more from Stripe Radar and ChargePay proactive fraud prevention tools.

Fee structure & transaction fees

The cost of payment processing is a key factor when choosing between Shopify Payments and Stripe.

Shopify Payments has a tiered fee structure based on the Shopify plan a merchant uses:

• Basic Shopify: 2.9% + 30¢ per online transaction
• Shopify Plan: 2.6% + 30¢ per online transaction
• Advanced Shopify: 2.4% + 30¢ per online transaction

One major advantage of Shopify Payments is that it eliminates the additional 0.5% – 2% transaction fees 

Shopify charges merchants who use third-party gateways like Stripe or PayPal. 

However, businesses processing international transactions may incur currency conversion fees of 1.5% – 2%, which can add up over time.

Stripe, on the other hand, charges a flat rate of 2.9% + 30¢ per online transaction, regardless of the business size. 

Unlike Shopify Payments, Stripe does not charge additional fees for using the platform on multiple websites. However, international transactions are subject to an additional 1% fee if currency conversion is required.

For Shopify-exclusive businesses, Shopify Payments can be more cost-effective, as it removes additional Shopify transaction fees. 

However, for businesses selling on multiple platforms, Stripe’s consistent pricing and flexible integration make it a better choice.

Shopify Payments vs Stripe: Which is preferable for your business

Choosing between Shopify Payments vs Stripe depends on your business model and needs. 

If you operate exclusively on Shopify, Shopify Payments offers a seamless experience with lower overall costs, direct integration, and built-in analytics. 

However, its availability is limited to certain countries, and merchants selling internationally may face higher currency conversion fees.

On the other hand, Stripe is ideal for businesses needing more flexibility. 

It integrates with multiple platforms, provides advanced fraud protection, and offers customizable payment solutions through its powerful API. 

While it does not eliminate Shopify’s extra transaction fees, it is the better choice for businesses operating beyond Shopify or requiring advanced payment customization.