Best Alternative Payment Gateway Options for Shopify

Introduction

Choosing the right payment provider is a balance between global reach and local relevance. While many merchants start with Shopify’s default processor, business growth often often requires more specialized solutions. An alternative payment gateway for Shopify becomes necessary when you expand into new regions, sell high-risk products, or want to reduce transaction fees.

The checkout experience is where your hard-earned traffic turns into revenue. If a customer reaches the final step and doesn't see their preferred payment method—or feels redirected to an unfamiliar third-party site—they often abandon their cart. At Nextools, we understand that managing these multiple options can become complex. We built HidePay to help merchants take back control of their checkout by hiding, sorting, or renaming payment methods based on specific logic — you can get HidePay for your store.

This guide explores the top alternative gateways, why you might need them, and how to manage them to maximize your conversion rates. Whether you are dealing with regional restrictions or seeking lower fees, selecting the right alternative is a strategic move for your bottom line.

Why Merchants Move Beyond Shopify Payments

Shopify Payments is a robust tool powered by Stripe, but it is not a universal fit. Several factors drive successful stores to integrate alternative providers.

Regional Availability and Localization

The most common reason for seeking an alternative is geography. Shopify Payments is only available in certain countries. If your business is registered in a country outside of this supported list, you must use a third-party gateway. Even if you are in a supported region, local customers often prefer specific methods. For instance, shoppers in the Netherlands rely heavily on iDEAL, while those in Spain frequently use Bizum. If your primary gateway does not support these, you lose sales.

High-Risk Industries

Certain product categories are prohibited by the terms of service of many mainstream processors. This often includes items like CBD, tobacco, alcohol, or high-value jewelry. If you sell in these niches, you require a high-risk payment gateway that understands your industry. These providers offer more stable accounts and are less likely to freeze your funds during a sudden sales spike.

Transaction Fees and Margins

Profit margins are under constant pressure. While Shopify Payments offers competitive rates, some alternative gateways offer volume-based discounts. Large-scale merchants often find that a fraction of a percentage point in savings adds up to thousands of dollars per month. Additionally, when you use a third-party gateway, Shopify typically charges an additional transaction fee unless you use their native processor. You must calculate whether the gateway's lower rates offset this additional cost.

Checkout Control

Some gateways offer a "direct" integration, meaning the customer stays on your domain throughout the entire process. Others use "external" redirects, sending the user to another page to enter their details. Most merchants prefer direct integrations because they maintain brand trust and reduce the friction that leads to cart abandonment.

Direct vs. External Payment Gateways

Understanding the technical difference between these two integration types is vital for your user experience.

Direct Gateways

A direct gateway handles the transaction within your Shopify checkout. The customer enters their credit card information directly into the fields on your site. This is the gold standard for conversion. It feels professional and keeps the user focused on the purchase. Popular direct alternatives include Stripe, Adyen, and Worldpay.

External Gateways

External providers redirect the customer away from your store to a secure payment page hosted by the provider. Once the payment is complete, the user is sent back to your "Thank You" page. While this is secure, it adds a step and a change in visual branding. If the redirect page looks outdated or untrustworthy, customers may hesitate. However, for certain local payment methods or high-risk niches, external gateways are sometimes the only viable option.

Top Alternative Payment Gateways for Shopify

Selecting the right provider depends on your specific business needs. Here are the leading contenders in the current market.

1. Stripe

Stripe is a powerhouse in the e-commerce world. It offers a highly customizable API and supports hundreds of currencies and local payment methods. Many merchants choose Stripe independently of Shopify Payments because of its advanced reporting and developer-friendly tools. It is an excellent choice for businesses looking to scale internationally with a direct integration.

2. PayPal

PayPal is one of the most recognized names in online payments. For many customers, the presence of a PayPal button provides an immediate sense of security. It offers both direct credit card processing and the familiar "Express Checkout" button. While their transaction fees can be higher than competitors, the trust factor often justifies the cost.

3. Adyen

Adyen is built for large enterprises and high-volume merchants. It supports a massive range of global payment methods through a single integration. One of its standout features is its advanced fraud protection and "smart routing" capabilities. If you are running a complex international operation with multiple entities, Adyen is a top-tier choice.

4. MONEI

MONEI is a particularly strong alternative for merchants operating in Europe, especially Spain and Andorra. It allows you to accept local methods like Bizum and Bancontact alongside standard credit cards. They use a dynamic billing system where your fees decrease as your sales volume increases, making it a favorite for growing brands.

5. Klarna and Afterpay (BNPL)

While technically "Buy Now, Pay Later" (BNPL) services, these function as alternative gateways at checkout. They allow customers to split payments into installments. Offering BNPL can significantly increase average order value (AOV), especially for fashion and electronics brands catering to younger demographics.

Managing Multiple Gateways with HidePay

As you add more payment options to satisfy different customer segments, your checkout can quickly become cluttered. Too many choices lead to "decision paralysis." This is where we help you optimize the experience.

HidePay allows you to create rules that control exactly which payment methods appear for which customers. Instead of showing every gateway to everyone, you can use logic to refine the list. For example, if you offer a high-cost payment method with high processing fees, you might choose to hide it for low-value orders to protect your margins.

You can also use the app to sort your payment methods. Putting your most cost-effective or highest-converting option at the top of the list encourages customers to choose it. If you have a B2B segment, you can use customer tags to show them "Pay by Invoice" while hiding that option for standard retail customers. This level of precision ensures your checkout remains clean and functional — read the guide on how to create a payment customization if you want step-by-step setup instructions.

Strategic Use Cases for Payment Rules

• Geography-based Hiding: If a specific gateway doesn't support a certain currency or region, hide it for those customers to prevent error messages at the final step.
• Product-specific Rules: If you sell digital products alongside physical goods, you might want to hide certain methods for digital downloads to prevent fraud or chargebacks.
• Express Checkout Management: Sometimes express buttons like Apple Pay or PayPal can interfere with your upsell apps or custom scripts. We allow you to block these buttons based on specific cart conditions — learn more about hiding the Express Checkout with HidePay.
• Risk Mitigation: Hide payment methods that are known for high chargeback rates when a customer's cart total exceeds a certain amount.

How to Choose the Right Gateway for Your Store

Do not rush into a contract with a payment provider without vetting them against your specific business requirements.

Step 1: Check Compatibility

Before looking at fees, verify that the gateway integrates with Shopify in your specific country. Shopify maintains a list of supported providers for each region in their official documentation. Ensure the gateway supports "Direct" integration if maintaining a consistent checkout brand is a priority for you.

Step 2: Analyze the Fee Structure

Most gateways charge a percentage of the transaction plus a fixed cent fee. However, you must also account for setup fees, monthly fees, chargeback fees, and international/currency conversion fees.

Step 3: Evaluate the Security and Fraud Tools

Chargebacks can kill a small business. Look for gateways that offer robust fraud detection, 3D Secure verification, and real-time monitoring. Some providers, like Adyen and Stripe, have highly sophisticated machine-learning tools that block suspicious transactions before they even reach your store.

Step 4: Test the Support

When your checkout goes down, every minute costs money. Reach out to the provider’s support team before signing up. See how quickly they respond and whether they provide technical answers or generic canned responses.

Optimizing the Checkout Flow

Once you have your alternative gateways installed, the work isn't over. You need to ensure they are presented in a way that maximizes conversion.

A common mistake is simply listing gateways in the order they were installed. This is rarely the best strategy. Use the sorting features in our app to place the most trusted and easiest-to-use methods at the top. For most stores, this means placing credit card options first, followed by express options like PayPal or Apple Pay.

You should also consider the names of your payment methods. Sometimes, a gateway's default name is confusing to the end-user. HidePay lets you rename these options. Instead of a technical provider name, you can rename it to "Credit / Debit Card (Secure)" to give the customer more confidence — see the HidePay instructions on sorting and renaming payment methods.

Action Plan for Merchants

1. Audit your current fees: Determine if you are overpaying for your current volume.
2. Identify missing methods: Research which local payment methods your top three target countries prefer.
3. Install a secondary gateway: Always have a backup in case your primary provider experiences an outage or freezes your account.
4. Implement HidePay: Use our tool to clean up the checkout and ensure only the most relevant, high-converting options are visible.
5. Monitor conversion rates: Check your Shopify analytics to see if the new gateway configuration improves your checkout completion rate.

The Role of Shopify Functions

The technology behind checkout customization has changed significantly. Previously, merchants had to use "Shopify Scripts," which required a Shopify Plus subscription and complex coding. Today, we use Native Shopify Functions.

HidePay is built on these functions, which means our app runs natively within the Shopify infrastructure. This transition is important because it offers better performance and reliability. Functions do not rely on theme code edits or external workarounds. This ensures that your checkout remains fast and secure, even during high-traffic events like Black Friday. If you’re interested in the broader context of migrating from Scripts to Functions, check the Nextools blog post on why Shopify Functions are the future. For merchants who want to generate or migrate Functions without coding, consider the codeless tool SupaEasy on the Shopify App Store.

Protecting Your Bottom Line

Every decision regarding your payment stack should serve two purposes: increasing conversion and protecting your margin.

If you ship bulky items that are expensive to return, you might want to hide "Cash on Delivery" or certain BNPL options that have high return rates. By using rule-based logic, you are not just making the checkout look better; you are actively managing the financial risk of your business. If the issue also involves shipping method choices, you can complement payment rules with shipping controls using [HideShip on the Shopify App Store].(https://apps.shopify.com/hideship)

Choosing an alternative payment gateway for Shopify is only the first step. The real competitive advantage comes from how you manage those gateways. Sorting them to favor low-fee providers and hiding them to prevent high-risk transactions creates a leaner, more profitable operation.

We invite you to explore how these customizations can transform your store. Read our introductory article for more context on HidePay and checkout optimization: Introducing HidePay for Shopify.

Conclusion

Finding the right alternative payment gateway for Shopify is a fundamental part of scaling a global e-commerce business. Whether you are moving away from the default provider due to regional restrictions, high-risk product requirements, or a desire for better transaction rates, the options are plentiful.

The key takeaways for optimizing your payments are:

• Identify the preferred local payment methods for your primary markets.
• Differentiate between direct and external gateways to protect your user experience.
• Calculate the total cost of ownership, including Shopify’s third-party transaction fees.
• Use logic to hide or sort methods to reduce friction and protect your margins.

By taking control of your checkout, you remove the barriers that stand between your customers and a completed purchase. Ready to optimize your checkout experience? You can install HidePay from the Shopify App Store today and start building a smarter, more efficient payment flow.

FAQ

Can I use multiple alternative payment gateways on Shopify at the same time?

Yes, Shopify allows you to enable multiple payment providers. You can have a primary credit card processor, several "Buy Now, Pay Later" options, and digital wallets like PayPal. However, having too many visible options can clutter your checkout, so it is often best to use an app to hide or sort them based on the customer's location or cart value.

Does using an alternative gateway increase my transaction fees?

If you do not use Shopify Payments, Shopify typically charges an additional transaction fee for every order processed through a third-party gateway. You should compare the rates of the alternative provider to see if their lower processing fees offset this additional cost from Shopify.

Why would I want to hide a payment method for certain customers?

Merchants often hide payment methods to reduce costs or risk. For example, you might hide a gateway with high processing fees for small orders or hide "Cash on Delivery" for customers in regions where shipping returns are expensive. You can also hide specific gateways for high-risk products that are not covered by that provider's terms of service.

Is it possible to change the order in which payment methods appear at checkout?

By default, Shopify does not allow you to easily reorder payment methods in the admin settings. However, using HidePay, you can set sorting rules to ensure your preferred or most cost-effective payment methods appear at the top of the list, encouraging customers to choose them over more expensive options. For detailed steps on sorting and renaming, see the HidePay help article on Sort and Rename payment methods in the Checkout.