4 Best Shopify Payments Alternatives

While I appreciate Shopify Payments, I like to keep my options open. Plus, some industries aren’t a great fit for this payment gateway. So, I’ve put together a list of alternatives.

We chose Stripe as the best overall alternative. Why? Because its chargeback protection covers digital products. Something Shopify Payments doesn’t offer. Stripe also provides advanced tools for sellers, like subscription management and Stripe Radar.

I’ll break these features down later.

But what if you’re a high-risk seller or need to reach international buyers? Don’t worry — I’ll provide suggestions for those as well. So, keep reading.

Let’s begin by comparing these alternatives.

Alternatives for Shopify Payments to Consider

1. Stripe: Best overall
2. Authorize.net: Best for sellers in high-risk industries
3. Square: Best for selling both in-person and online
4. Adyen: Best for payment method availability

I’ll dive deeper into each option. But first, I recommend checking out the buying guide at the end of this post. It’ll help you decide which gateway aligns best with your business needs.

You won’t see PayPal on this list. Why? Because you can use PayPal and Shopify Payments simultaneously. That means it’s not technically an “alternative” to Shopify Payments.

If you’re looking for gateways that support cryptocurrency, I cover that in a separate guide. Check it out for suggestions and tips.

Regardless of which processor you choose, chargebacks are always a risk. Too many of them can lead to higher fees. Or even losing your account with the gateway.

One of the best ways to prevent chargebacks is by using chargeback alerts. These alerts notify you before a dispute is filed, giving you the chance to resolve the issue directly with the customer.

We offer chargeback alerts that integrate seamlessly with Shopify. Learn more about how they work.

Now, let’s dive into our top pick. Stripe.

1. Stripe: Best Overall

Who should get it: SMBs selling digital goods with up to $25,000 in annual chargeback protection. It’s also ideal for businesses in Mexico, as Stripe reimburses won chargebacks there. Subscription-based businesses and those needing custom payment portals will benefit too.

Pros:

• Easier chargeback management.
• Accepts 135+ currencies.
• Supports more payment methods.
• Highly customizable for advanced users.

Cons:

• Chargeback protection isn’t available in many countries.
• Poor option for in-person payment processing.
• Additional costs for chargeback prevention and protection tools.

Stripe’s ability to accept over 135 currencies makes it a stronger choice than Shopify Payments for sellers targeting international markets. This is especially true if you’re selling outside Shopify Payments’ limited list of supported countries.

However:

It’s not ideal for in-person sales, as Stripe requires you to build custom POS software. If you need an easier solution, I recommend PayPal or Square. I’ll explain why later.

Both Shopify Payments and Stripe simplify the checkout process with one-click payment tools. Shopify Payments uses Shop Pay, while Stripe uses Link.

If frictionless checkout is important, both platforms deliver on that front.

This is a website that talks about chargebacks so by law we need to talk about chargebacks. Kidding. 

Using Stripe as a separate payment processor means managing Stripe chargebacks on their platform. Not within Shopify. That also means losing Shopify Payments’ chargeback fee reimbursement.

If you’re a business in Mexico, Stripe offers reimbursement for won chargebacks

What happens if your chargeback rate gets too high?

Shopify Payments isn’t clear about their policies, but reports suggest some sellers lose their accounts for high chargeback rates. Stripe may implement a rolling reserve. This means they’ll hold a portion of your earnings as a buffer to cover disputes and refunds.

We discuss rolling reserves in more detail in a separate guide. You should also check out our Stripe-specific chargeback guide to better understand how they handle disputes.

Every processor has its own rules. Thus, it’s critical to know how Stripe operates.

Does Stripe have a chargeback rate threshold? They don’t state one publicly, but keeping your chargeback rate below 0.65% is a safe bet. This minimizes your risk of issues with Stripe.

Part of lowering your rates involves chargeback prevention.

Stripe excels in chargeback prevention, thanks to tools like Stripe Radar. This fraud detection system costs an additional $0.05 per screened transaction, but it’s effective. It has reportedly blocked 16.7 million fraudulent transactions, with a false positive rate of only 0.1%.

Stripe also offers 3D Secure, which adds an extra verification layer for online payments. It costs $0.03 per attempt plus the transaction fee. By comparison, Shopify Payments includes 3D Secure and fraud scoring at no extra cost.

Stripe’s tools are powerful. Though, the additional fees for fraud prevention and chargeback protection can add up, especially for smaller businesses. Consider this when deciding if Stripe is the right fit for you.

Fees:

• Subscription: None
• Chargeback fee: $15
• Payment processing: 2.9% + 30¢ (Standard)
• Chargeback protection: 0.4% per transaction

Accepted payment methods:

What should you do if Stripe doesn’t allow you to open an account with them? I might have a solution.

2. Authorize.net: Best for High-Risk Businesses

Who should get it: High-risk merchants in the US, UK, Canada, Europe, and Australia.

Pros:

• Reasonable transaction fees for a high-risk processor.
• Accepts high-risk sellers.

Cons:

• Only available in the US, CA, UK, EU, and AU.
• $25/month subscription fee.
• Doesn’t support 3D Secure.

If you’re in a high-risk (but legal) industry that other gateways won’t touch, Authorize.net is a solid option. So long as you’re operating in one of the supported regions. If you’re outside these areas, you’ll need to find a high-risk processor in your country.

Shopify staff have recommended the following alternatives [1]:

• Merchant Account Providers
• SecurePay
• 2Checkout (the only option available in India)
• Bankful (also supports crypto)

I haven’t personally vetted these options but included them as suggestions for you to explore. If you’re unsure what’s available in your area, follow this link on Shopify’s site. From there, select your country to see a list of supported gateways.

Usually high-risk processors come with additional fees. Since they’re taking on additional risk from “sketchy” sellers. This price comes in the form of a $25-a-month subscription that goes on top of your Shopify sub.

And if you have a chargeback, you’ll pay a $25 fee. This is on the high-end of dispute fees. And it isn’t refundable if you win a chargeback. Though, the majority of processors won’t reimburse this.

If your industry is prone to high chargeback rates, or if this is the reason you’re categorized as high-risk, you’ll need to reduce disputes. Failure to do so could lead to restrictions on your account. Or worse, being placed on the MATCH list, which is a blacklist for payment processors.

From what I’ve heard, maintaining a chargeback rate above 1% could result in losing access to Authorize.net.

Ways to lower your rates include using chargeback alerts, improving your SOPs and QA, and more. We cover a bunch of ways to prevent chargebacks in a different guide.

Authorize.net does offer “advanced” fraud detection tools. It’s nothing that stands out compared to competitors, though. They also don’t provide chargeback insurance. You’ll need a third-party provider for that.

Fees:

• Subscription: $25/mo
• Chargeback fee: $25
• Payment processing: 2.9% + $0.30

Accepted payment methods:

You’ll want a different processor if you’re not a high-risk merchant and want to sell in-person.

3. Square: Best Omnichannel Processor

Who should get it: Merchants selling in-person or those in low-risk industries with products prone to chargebacks.

Pros:

• No chargeback fees.
• Available in regions where Shopify isn’t (e.g., France, Japan).
• Basic card payment software is free.

Cons:

• No chargeback protection.
• Pricing isn’t competitive for larger businesses.

Number of merchants & transactions: Square serves more than 4 million sellers. It also processed $112.3 billion in payment volume in 2023.

Square is a good choice if you’re primarily focused on in-person sales. Their basic software for accepting card payments is free. Though, larger retailers may need to pay extra for advanced features via a subscription.

Want a card chip reader?

You’ll need to pay separately, and it’s highly recommended. Why? Because relying on the included magstripe reader puts you at risk of losing EMV liability shift in fraud cases. Magstripe technology is outdated and easier to hack. Thus, a chip reader is much safer.

For comparison, Shopify’s basic card reader costs $49, while Square’s reader costs $59. Both platforms charge similar fees for in-person purchases. Hardware and subscription features may determine which is the better option for your business.

Okay, so why recommend Square?

Square has some advantages over Shopify POS in certain regions. Shopify’s POS system isn’t available in France or Japan. Sellers in those countries will find Square more useful. Meanwhile, merchants in places like Singapore would be better off with Shopify.

Their handling of chargebacks may also make it appealing. Unlike most processors, Square doesn’t charge fees for chargebacks. This can save businesses thousands annually. Instead, Square compensates for this by charging slightly higher transaction fees.

How does Square deal with them? The same as most processors. They have a chargeback process you’d do outside of Shopify through Square’s dashboard.

There’s a tradeoff.

No chargeback protection. For fraudulent chargebacks, Square doesn’t offer insurance to cover the cost of the disputed item. Many other platforms provide this protection. This is a big drawback for businesses prone to disputes.

Square is best for in-person purchases. Why? Because EMV technology has reduced in-person fraud by 80%. By contrast, card-not-present fraud (e.g., online purchases) has increased by 81%. Without strong fraud protections, Square is risky for online sales.

If you must use Square for online purchases, consider third-party fraud protection tools like Signifyd. However, these tools can be costly. Alternatively, you could test Square’s Risk Manager, a fraud scoring tool.

I couldn’t find data on its effectiveness or false positives. Use it cautiously.

Fees

• Subscription: NA
• Chargeback fee: None
• Payment processing:
  • 2.9% + 30 cents (online)
  • 2.6% + 10 cents (in-person)

Accepted payment methods:

We’ve got one more alternative for you.

4. Adyen: Best for Multiple Payment Options

Who should get it: Super high-volume businesses looking to save on costs and offer a wide variety of payment options.

Pros:

• Low chargeback fees.
• No monthly fees.
• Flexible pricing options.
• Supports over 180 currencies.

Cons:

• Pricing can be complex.
• Only suitable for high-volume businesses.
• Difficult to integrate without technical expertise.

Number of merchants & transactions: Around 10,000 merchants use Adyen, which processed €970.1 billion in payments in 2023.

Adyen is a fantastic choice for businesses with high transaction volumes. Its pricing is highly competitive. Especially when cycling between interchange-plus and flat-rate pricing models. This flexibility can help businesses save on transaction fees across more than 100 payment methods.

But beware: Adyen’s pricing structure is complicated. Seriously. I got a migraine just reading through it. If you prefer simpler, more predictable fees, Adyen might not be the right fit.

There are no hidden fees.

Adyen doesn’t charge for PCI compliance or account setup. Though, these benefits come with a catch. You must process at least 1,000 transactions per month to stay in good standing. Businesses with lower volumes might lose access to the platform.

Adyen’s integration isn’t beginner-friendly, either. Grabbing an API key is simple. Getting started requires using command line code. Such a task can be intimidating for non-technical users. For advanced customization, you’ll need more technical expertise.

If ease of use is a priority, Stripe is a better alternative. It’s much more user-friendly to set up and manage.

Let’s talk chargebacks (because I can’t stop).

Adyen shines in this area. It will automatically dispute certain chargebacks for you. Particularly those involving liability shift reason codes. This automation saves time and money by reducing the need to delegate staff to handle disputes.

But doesn’t automating disputes increase the risk of losing? Not really. Adyen’s system focuses on cases you’re more likely to win.

Adyen also has lower chargeback fees than most competitors. About half the price of many. This makes it a strong option for high-volume merchants who are otherwise burdened by chargeback costs.

Adyen’s RevenueProtect is an excellent fraud scoring tool with an intuitive user interface. Making it easier for businesses to automate risk management.

Adyen also offers an A/B testing tool. This feature allows you to test different risk profiles. That way, you'll find the best balance between preventing fraud and minimizing false positives.

Fees:

• Subscription: NA
• Chargeback fee: $10
• Payment processing: Varies by payment method

Accepted payment methods:

Find all the payment methods accepted and their fees here.

Should you bother looking for an alternative?

Why Choose an Alternative to Shopify Payments?

Here’s a closer look at why some merchants might explore alternatives — and the nuances behind this decision.

1. Availability

Shopify Payments is available in only 23 countries, leaving merchants in many regions to seek alternatives. If your business operates outside these supported regions, Shopify Payments simply isn’t an option.

What if you’re in a region that supports it? Then, consider the costs.

2. Fees

Processing fees can greatly affect your profits, and Shopify Payments isn’t always the cheapest option.

Some alternatives offer more competitive rates that can save you money. Especially on high-volume sales.

Switching from Shopify Payments may help you reduce payment processing expenses. This is especially important for businesses with large transaction volumes, where even small fee differences add up.

But there are trade-offs.

Shopify Payments includes perks like cheaper chargeback fees and potential chargeback refunds for eligible transactions. These benefits disappear if you switch to another processor. Weigh the savings carefully.

Speaking of chargebacks: having too many on Shopify Payments could lead to losing your entire Shopify account, not just access to the payment processor. Switching to a third-party gateway avoids this risk.

Do the fees Shopify Payments incur justify the features offered?

3. Features

Some payment gateways offer features that Shopify Payments lacks.

For example:

• Subscription billing: A must-have for businesses with recurring services or products, like memberships or subscription boxes.
• Advanced fraud detection: Better tools for high-risk industries or merchants with significant international sales.

Shopify Payments does include basic fraud protection for US merchants selling physical products. Though, other businesses may need more robust options.

That said, Shopify plugins can fill some of these gaps. However, plugins often come with extra costs and require you to manage additional accounts. If you’re looking for fraud protection in particular, we compared a list of great plugins here.

Payments could just not be compatible with your business.

4. Business Model Compatibility

Certain business models need specialized payment solutions that Shopify Payments doesn’t support.

For example:

• High-risk businesses: Industries like gambling or CBD struggle to find processors due to perceived risks.
  • High-risk providers offer tailored rates and services to address this.
• Consumer preferences: 76% of consumers will abandon a transaction if their preferred payment method isn’t available.

Offering a diverse range of payment options is essential for reducing cart abandonment and increasing conversions. Some alternative gateways also support local payment methods that Shopify Payments doesn’t. Helping you better serve your target audience.

Did you help yourself choose the right alternative, though?

How to Choose the Right Alternative

When picking a payment gateway, consider these key factors:

• Gateway Type: Hosted, API-hosted, self-hosted, or local bank integration.
• Payment methods: Credit cards, digital wallets, and BNPL options.
• International support: Currencies and local payment methods.
• Features: Customization, reporting, and multi-channel support.
• Fees: Transaction, currency conversion, and hidden costs.
• Chargebacks: How disputes and fees are managed.
• Reliability: Uptime and quality of customer support.
• Security: Compliance and fraud prevention tools.

I won’t cover all these points in this guide, but I’ve already gone into detail about them in my Shopify Payment gateways comparison piece. Check it out — it’s worth the read.

Let’s finish this.

Conclusion

If Shopify Payments doesn’t work for your business, there are plenty of alternatives to explore. Each option has its own pros and cons, so there’s no “perfect” gateway. But hopefully, this guide helped you find a solid alternative.

That said, no matter which gateway you choose, chargebacks will always be a concern. On average, they can cost businesses up to 20% of their revenue [2].

The best solution? Prevent them before they happen.

Our chargeback alerts can help keep your rates low and protect your revenue. Learn more about how they work. See how they’ll make a difference for your business.

Sources

• [1] Searching for a high risk payment gateway. Shopify. 10/30/2023.
• [2] What Do Chargebacks Cost? ClearSale. 08/30/2024.