What Payment Methods Does Shopify Use for Checkouts

Introduction

Choosing the right payment methods directly affects your store's conversion rate and bottom line. When your checkout offers the specific options your customers trust, you reduce friction and lower the chances of cart abandonment. Shopify provides a diverse range of built-in and third-party options to ensure every merchant can accept payments regardless of their location or business model.

We developed HidePay to give you complete control over how these methods appear to your customers — if you want to jump straight in, you can get HidePay for your store. While Shopify offers the infrastructure to accept payments, managing the visibility of those methods based on order value, shipping address, or customer type is what separates a standard store from a high-performance one.

This article covers the primary payment methods Shopify supports, the costs associated with them, and how you can strategically organize your checkout for maximum efficiency. Whether you are a new merchant setting up your first gateway or an established brand looking to optimize international sales, understanding these options is the first step toward a more profitable checkout.

Shopify Payments: The Native Solution

Shopify Payments is the platform’s own integrated payment processor. It is the most common choice for merchants because it removes the need to integrate third-party gateways. When you use this native solution, you automatically gain the ability to accept all major credit card brands, including Visa, Mastercard, American Express, and Discover.

The primary advantage of using the native system is the elimination of additional transaction fees. While you still pay the standard credit card processing rate based on your Shopify plan, you avoid the extra 0.5% to 2.0% fee that Shopify charges when you use external gateways. This makes it the most cost-effective option for businesses in supported regions.

Beyond credit cards, the native processor supports localized payment methods. For example, merchants in the Eurozone can accept iDEAL or Bancontact, while those in the United Kingdom can offer Clearpay. All of these transactions are managed within your Shopify admin, providing a single location for payouts and financial reporting.

Accelerated Checkouts and Express Buttons

Speed is a critical factor in mobile commerce. Accelerated checkouts, often called express buttons, allow returning customers to bypass manual data entry. They store the customer's shipping and billing information, reducing the checkout process to a single click or a biometric scan.

Many merchants use HidePay to hide or block specific express buttons when they clutter the experience — you can see how to hide the Express Checkout with HidePay.

Shop Pay

Shop Pay is Shopify’s proprietary accelerated checkout. It is known for its high conversion rates, as it allows customers to save their details across all stores that use the service. When a customer enters their email, they receive a six-digit verification code to their phone, which instantly populates their payment and shipping information.

Digital Wallets

Shopify also supports the world's most popular digital wallets:

• Apple Pay: Essential for iOS users, allowing for FaceID or TouchID verification.
• Google Pay: The standard for Android and Chrome users.
• PayPal Express: A trusted global option that lets customers use their PayPal balance or linked cards.
• Amazon Pay: Allows customers to use the payment methods already stored in their Amazon accounts.

While these buttons increase speed, they can sometimes clutter the top of your checkout page. Many merchants use our tool to hide specific express buttons for certain products or order types to ensure the customer journey remains focused.

Alternative Payment Methods (APMs)

As the e-commerce landscape evolves, traditional credit cards are no longer the only way customers want to pay. Alternative Payment Methods have become standard requirements for global stores.

Buy Now, Pay Later (BNPL)

BNPL services allow customers to split their purchase into interest-free installments. This is particularly effective for high-ticket items. Common providers integrated with Shopify include:

• Shop Pay Installments: The native BNPL solution.
• Klarna: Highly popular in Europe and North America.
• Affirm and Afterpay: Widely used in the US and Australia.

BNPL providers typically charge higher merchant fees, often ranging from 2% to 8%. However, they frequently increase the average order value because customers feel more comfortable making larger purchases when the cost is spread out.

Cryptocurrency

Shopify allows merchants to accept various cryptocurrencies by integrating with providers like Coinbase Commerce, BitPay, or Crypto.com. These payments are irreversible, which eliminates the risk of chargebacks for the merchant. This is a significant benefit for high-risk industries or international sales where traditional card fraud is more common.

Manual Payment Methods

Not every transaction happens through a digital gateway. Manual payment methods are those where the payment is processed outside of your online store. These are particularly useful for B2B businesses or regions where digital payment penetration is low.

Common manual methods include:

• Cash on Delivery (COD): The customer pays the courier upon arrival.
• Bank Deposits: You provide your bank details, and the customer initiates a transfer.
• Money Orders: A physical payment sent via mail or carrier.

The challenge with manual methods is that Shopify cannot automatically verify if the payment was received. You must manually mark these orders as "Paid" in your admin. Because COD often has a higher return-to-origin rate, we frequently see merchants using HidePay to hide the COD option for specific zip codes or risky customers — learn how to manage payment methods based on zip codes.

Third-Party Payment Gateways

If Shopify Payments is not available in your country, or if your business operates in a high-risk category that the native processor does not support, you must use a third-party gateway. There are over 100 providers available globally, including Stripe, Authorize.net, and 2Checkout.

When using a third-party gateway, you must consider two sets of fees:

1. Gateway Fees: What the provider (e.g., Stripe) charges you per transaction.
2. Shopify Transaction Fees: An additional percentage charged by Shopify for not using their native processor.

Before committing to an external provider, check the availability in your region and compare the total cost of ownership. Some gateways offer specialized features, like advanced fraud protection or support for niche currencies, which might justify the extra transaction fees.

Sorting and Renaming for Better UX

Having the right payment methods is only half the battle; how you present them matters just as much. By default, Shopify often displays payment methods in a fixed order. However, you can guide customer behavior by reordering these choices.

For example, if you prefer customers to use a method with lower processing fees, you can move that option to the top. If a payment method has a confusing name—such as a third-party gateway that doesn't clearly state it accepts credit cards—you can rename it to "Credit / Debit Card" to provide clarity for the shopper.

This level of customization reduces "choice paralysis." When a customer sees exactly what they expect, labeled clearly and in a logical order, they are much less likely to exit the checkout page. To learn the exact steps, see our guide on how to sort and rename payment methods.

Geographic and Currency Considerations

Shopify allows you to sell in multiple currencies, but your payment methods must support those currencies to function correctly. If you sell globally, you need to ensure that your checkout adapts to the user's location. For tips on translating and localizing checkout labels and delivery/payment text, read Translate Checkout Delivery & Payment Options.

In Germany, customers often look for SEPA Direct Debit. In the Netherlands, iDEAL is the dominant player. If you show a US-centric checkout to a European customer, you risk looking untrustworthy or inconvenient.

Shipping and payment choices are tightly related — if you need the same rule-based approach for shipping methods (for example, hiding expensive carrier options for certain zones), consider HideShip on the Shopify App Store to match payments and delivery logic.

Protecting Your Bottom Line with Rules

Optimization is not just about adding more options; it is about removing the wrong ones. Every payment method carries a different level of risk and cost.

• Reduce Chargebacks: If you notice a high volume of fraudulent chargebacks from a specific payment type, you can set a rule to hide that method for high-risk order values or specific customer tags.
• Manage Processing Fees: You might want to hide BNPL options for small orders where the high percentage fee eats too much of your profit.
• B2B Customization: For wholesale customers, you might want to hide credit cards entirely and only show "Bank Transfer" or "Net 30" options.

Our app is built on native Shopify Functions, which means these rules run within Shopify's own infrastructure — see why Shopify Functions are the future for more on performance and reliability.

If you want to generate or migrate custom Shopify Functions without coding, Nextools' SupaEasy can help — learn more on the SupaEasy Shopify listing.

To create the actual rules in HidePay, follow the steps in our help guide on how to create a payment customization.

Action Summary for Merchants

To make the most of Shopify's payment methods, follow these steps:

• Audit your fees: Compare the cost of Shopify Payments against third-party gateways in your region.
• Check regional preferences: Research the top 3 payment methods for every country you ship to.
• Clean up the UI: Rename any confusingly labeled payment methods for better clarity.
• Implement conditional logic: Use rules to hide expensive or high-risk methods based on cart totals or customer tags — see how to create a payment customization.
• Test the flow: Regularly go through your own checkout as a customer to ensure the order and visibility of methods make sense.

FAQ

Can I use multiple payment gateways on Shopify?

You can use Shopify Payments alongside PayPal and other alternative payment methods like Klarna or Bitcoin. However, you can generally only use one primary credit card processor at a time. If you use a third-party gateway for credit cards, you cannot use Shopify Payments simultaneously for the same purpose.

Why are some payment methods hidden at checkout?

Payment methods may not appear if they do not support the customer's currency, if the store's address is in an unsupported region, or if the merchant has set up specific rules. If you are using an app to manage your checkout, check your active rules to see if any geography or cart-based conditions are hiding the method.

Does Shopify charge a fee for every payment method?

Shopify does not charge a transaction fee if you use Shopify Payments, Shop Pay, or manual methods like Cash on Delivery. If you choose to use a third-party gateway (like Stripe or Authorize.net) instead of Shopify Payments, an additional transaction fee of 0.5% to 2% will apply, depending on your subscription plan.

How do I change the order of payment methods on Shopify?

By default, Shopify determines the order of payment methods. To gain full control over the sequence, you need an app like HidePay. This allows you to sort methods so that your preferred or most popular options appear first, helping to streamline the customer experience.

Conclusion

Shopify offers a robust suite of payment options, from its native Shopify Payments system to dozens of third-party gateways and express checkout buttons. Success depends on selecting the methods that match your customers' expectations while protecting your store's margins. By strategically hiding, sorting, and renaming these options, you can create a checkout experience that feels local and trustworthy to every shopper.

To take full control of your checkout, consider these key steps:

• Identify which payment methods cause the most friction or highest fees.
• Tailor your checkout visibility to different customer segments.
• Use logic-based rules to automate your payment strategy.

Ready to optimize your checkout? Install HidePay from the Shopify App Store today to start building a more efficient, high-converting payment process.