What Payment Method Should I Use for Shopify?

Introduction

Choosing the right payment methods for your Shopify store directly impacts your conversion rate and your bottom line. While offering more choices can reduce friction, an cluttered checkout often leads to decision fatigue and abandoned carts. At Nextools, we developed HidePay to give you granular control over these options, ensuring that your customers only see the most relevant, cost-effective payment methods for their specific situation — you can install HidePay and start creating rules in minutes.

This guide outlines the best payment methods for different business models and regions. We will look at transaction fees, processing speeds, and risk factors associated with the most common gateways. Whether you are a local boutique or a global dropshipper, understanding how to curate your payment stack is essential for growth.

By the end of this article, you will have a clear framework for deciding which methods to activate. You will also learn how to optimize your checkout layout to prioritize the methods that convert best while protecting your margins.

The Foundation: Shopify Payments

For most merchants, the default starting point is Shopify Payments. This is the platform’s integrated gateway, powered by Stripe, which allows you to accept all major credit cards and digital wallets without the need for a separate third-party account.

The primary advantage of using the native gateway is the elimination of additional transaction fees. Shopify typically charges a transaction fee (ranging from 0.5% to 2.0%) if you use a third-party gateway like Authorize.net or 2Checkout. When you use the native provider, these fees are waived.

Key Benefits of the Native Gateway

• Centralized Management: You view your payouts and manage chargebacks directly within your Shopify admin.
• Speed of Setup: In most supported countries, you can start accepting payments almost immediately after providing your business details.
• Native Integration: It works perfectly with Shopify’s internal features, such as Shop Pay and local currency conversions.

If your business is located in a supported country (such as the US, UK, Canada, Australia, or many EU nations), this should almost always be your primary payment method. It covers the vast majority of customer preferences while keeping your operational costs predictable.

Accelerated Checkouts and Mobile Wallets

Mobile commerce now accounts for the majority of online traffic. To capture these users, you must offer accelerated checkout buttons. These options store a customer’s payment and shipping information, allowing them to complete a purchase with a single click or a biometric scan (like FaceID).

The most common accelerated methods include:

• Shop Pay: Shopify’s own accelerated checkout, which has been shown to increase conversion rates by up to 50% compared to guest checkouts.
• Apple Pay: Essential for iOS users. It is fast, secure, and highly trusted.
• Google Pay: The primary choice for Android and Chrome users.
• PayPal Express: A global standard that many customers prefer for the added layer of buyer protection.

While these buttons increase speed, they can sometimes create visual clutter on your product pages or the first step of checkout. We recommend using rules to display these only when they are most likely to be used. For example, you can use HidePay to hide express checkout buttons (or specific ones like Apple Pay) when they don’t apply to the shopper’s device or market — see the guide on how to hide Express Checkout buttons with HidePay.

Buy Now, Pay Later (BNPL) Options

Buy Now, Pay Later services like Klarna, Affirm, and Afterpay have seen massive adoption, particularly among younger demographics. These services allow customers to split their purchase into interest-free installments, while you, the merchant, receive the full payment upfront.

When to Use BNPL

If you sell high-ticket items (over $100), BNPL is almost mandatory. It lowers the barrier to entry for expensive purchases and can significantly increase your Average Order Value (AOV). If your audience is primarily Gen Z or Millennials, they may specifically look for these options as a budgeting tool.

The Downside: Higher Fees

The trade-off for higher conversion is higher merchant fees. While standard credit card processing fees usually hover between 2.4% and 2.9%, BNPL providers often charge between 5% and 8%.

If you have low margins, you might want to limit when these options appear. For example, you can set a rule in HidePay to only show BNPL options for orders above a threshold using a cart-total condition — see the help doc on creating payment customizations in HidePay for step-by-step instructions.

Regional Preferences and Local Methods

The answer to "what payment method should I use" changes dramatically depending on where your customers live. A checkout that works in New York will likely fail in Berlin or Manila.

Europe: Local Bank Transfers

In many European countries, credit cards are not the primary way people pay online.

• Germany: Customers heavily favor SOFORT and Giropay.
• Netherlands: iDEAL is the dominant player, used in over 60% of online transactions.
• Belgium: Bancontact is the standard.

If you are expanding into Europe, failing to offer these local bank transfer methods will lead to high abandonment rates.

Southeast Asia and Latin America: Cash on Delivery

In markets with lower credit card penetration, Cash on Delivery (COD) is often the only way to reach a mass audience. However, COD carries significant risks for the merchant, including high refusal rates upon delivery and delayed cash flow.

If you ship to these regions, you should use geographic rules to manage COD. For a concrete example of hiding COD for expensive orders (cart-total rules), see the tutorial on preventing fraud by hiding Cash on Delivery.

Managing Risks and High Fees

Every payment method carries a different level of risk. Credit cards and PayPal are susceptible to chargebacks, while bank transfers are generally irreversible. As a merchant, you must balance customer convenience with your own safety.

Reducing Chargebacks

If you are seeing a high volume of fraudulent chargebacks on certain types of products (like digital goods or high-end electronics), you might choose to hide specific payment methods for those items. You can create a rule that hides PayPal for specific high-risk product tags — follow the step-by-step in how to hide payment methods when certain products are in the cart.

Protecting Your Margins

Some payment methods are simply too expensive for low-cost items. If you sell a $5 sticker, a payment method with a high flat fee (like $0.30 + 5%) might eat your entire profit. In this scenario, you can use HidePay to hide expensive payment methods for small cart totals and only show them when the order value makes the fee justifiable.

Strategic Sorting and Customization

The order in which payment methods appear at checkout matters more than most merchants realize. Customers often select the first option they see. If your first option is a high-fee method, you are losing money on every transaction.

How to Sort for Success

We recommend sorting your payment methods based on your business goals:

1. Lowest Fee First: If your margins are tight, put your lowest-fee method (often Shopify Payments) at the top.
2. Highest Conversion First: If you are struggling with abandonment, put the fastest methods (Shop Pay or Apple Pay) at the top.
3. Local Trust First: If you are selling internationally, ensure the local hero method (like iDEAL in the Netherlands) is the first thing the customer sees.

Renaming for Clarity

Sometimes, the default name of a payment method is confusing. Shopify allows for "Manual Payment Methods," but calling something "Bank Deposit" might not sound professional. Using HidePay, you can rename these methods to something more descriptive, such as "B2B Net-30 Bank Transfer" or "Local QR Code Payment." For details on reordering and renaming payment methods, see the guide to sort and rename payment methods in HidePay.

The Technical Advantage of Shopify Functions

In the past, merchants had to use "Shopify Scripts" to modify the checkout experience. However, scripts were only available to Shopify Plus merchants and often slowed down the checkout page.

HidePay is built on native Shopify Functions, the modern and faster way to customize Shopify’s backend without heavy theme code. If you want the technical background on why Functions are superior to Scripts, read Nextools’ article on why Shopify Functions are the future.

Action Plan: Optimizing Your Checkout

Once you have decided which payment methods to use, follow these steps to refine your checkout:

• Review your analytics: Identify which payment methods currently have the highest abandonment rates and which have the highest fees.
• Segment your rules: Create geographic rules to show local payment methods only to customers in those regions.
• Set threshold limits: Use cart-total rules to hide high-fee BNPL options for small orders.
• Prioritize mobile: Use sorting rules to ensure digital wallets are at the top for mobile users.
• Test and iterate: Change one rule at a time and monitor your conversion rate for a few days before making further adjustments.

For a merchant-friendly overview of HidePay’s goals and capabilities, see the Nextools announcement introducing HidePay for Shopify.

Conclusion

The "best" payment method for your Shopify store is a combination of what your customers trust and what protects your margins. For most, a solid foundation consists of Shopify Payments, a few major digital wallets, and a regional BNPL provider. However, the real success comes from actively managing these options based on the customer’s location, cart value, and risk profile.

HidePay offers the control needed to turn a generic checkout into a high-converting, profit-protecting asset. By hiding irrelevant options, sorting by preference, and renaming for clarity, you create a professional experience that meets global customer expectations. If you are ready to take full control of your checkout and reduce unnecessary fees, get HidePay for your store and start building your custom payment rules.

FAQ

Can I hide PayPal for certain products on Shopify?

Yes, you can hide specific payment methods based on the contents of the customer's cart. This is useful for high-risk items or products with very low margins where PayPal's fees or chargeback policies might be a concern. See the tutorial on hiding payment methods when specific collections or products are in the cart for step-by-step instructions.

Is it possible to show different payment methods for different countries?

Absolutely. This is one of the most effective ways to use our app. You can create rules so that customers in the Netherlands see iDEAL, while customers in the United States see Shop Pay and credit card options. For details on creating geographic and cart-currency conditions, consult the HidePay guide on creating payment customizations.

Does hiding payment methods affect my site speed?

Because our tool is built using native Shopify Functions, it does not negatively impact your site's performance. The rules are processed directly by Shopify's infrastructure as the checkout page loads, ensuring a fast and responsive experience for your customers without the need for heavy external scripts. For more on how Functions replace Scripts, see the Nextools article on Shopify Functions vs. Scripts.

Can I reorder how payment methods appear at checkout?

Yes, you can sort your payment methods to ensure your preferred options appear first. Many merchants use this to place lower-fee methods at the top or to prioritize accelerated checkouts like Apple Pay for mobile users, which helps improve conversion rates and reduces processing costs. Review the step-by-step sort and rename payment methods guide to get started.