5 Best Shopify Payment Gateways

I’ve been using Shopify for years to sell my own products and have helped clients do the same. During this time, I’ve often wondered: what’s the best payment gateway? The answer depends on your needs. But in this piece, we’ll explore some great options.

For many, Shopify Payments is the best choice. Especially in the US. It handles chargebacks well, easily integrates with Shopify, and works well for selling physical products.

Not convinced? Don’t worry. We’ve got more recommendations for you. You can also check out our guide on the best Shopify Payments alternatives for other options.

Let’s kick things off by briefly comparing the top gateways.

Top Shopify Payment Gateways

• Shopify Payments: Best overall
• PayPal: Best for international payments and dropshippers.
• Authorize.net: Best for high-risk merchants
• Stripe: Best for subscription-based services
• Coinbase Commerce: Best for accepting cryptocurrency

I’ve also noticed a lot of interest from users in India looking for Shopify payment processors. If that’s you, I’ve included notes in a separate section. The research for this was a bit tricky, but I’ve got you covered.

Before diving into the list, I recommend checking out the buying guide at the end of this post. It explains what to look for in a gateway and helps you better evaluate the options.

Why isn’t the buying guide at the top? It’s long. Scrolling through it first might slow you down.

Ready? Let’s start with the best overall pick.

1. Shopify Payments: Best Overall

Who should get it: US merchants selling physical products. It offers chargeback protection, pretty low domestic transaction fees, and no need to manage separate integrations. It’s also a great option for dropshippers because of its chargeback fee reimbursement for physical goods.

Pros:

• If you win a dispute, Shopify refunds your chargeback fee.
• No need to log in to a separate platform.
• No limits on the amount you can process monthly.

Cons:

• Fewer options compared to other gateways.
• High international transaction and currency conversion fees.
• If you’re banned on Shopify Payments, you also may lose access to Shopify.

Number of merchants & transactions: Around 400,798 e-commerce stores have Shopify Payments installed [1]. The platform processed $18 billion in gross merchandise value (GMV).

Shopify Payments is best for merchants in the US because:

• Low(ish) domestic transaction fees.
• Chargeback fee reimbursement.
• Fraud protection for physical products.

If you sell luxury goods, these features are particularly helpful.

For many international sales, Shopify Payments isn’t ideal.

They charge 4.4% for transactions outside the US, plus currency conversion fees. That’s 1.5% for US-based transactions and 2% for most other regions. Additionally, sellers targeting France may face challenges. Shopify Payments restricts many currencies and payment methods in that region.

Chargebacks. We are a chargeback website, so we must talk about those.

Wait, what are chargebacks? Here’s a guide that’ll tell you everything.

Shopify Payments doesn’t have a chargeback threshold. But you should still keep your rates low to avoid being placed in monitoring programs. See this piece to understand what I mean.

The chargeback process isn’t anything special. What’s neat is that you can manage chargebacks through Shopify. And if you win the dispute, they’ll refund the chargeback fee. This is rare with payment gateways.

Think about this for context.

If you had an average transaction value of $18 and 24 chargebacks monthly, you could pay up to $7,056 a year in chargeback fees alone. That’s not including administrative fees (e.g., costs to fight disputes).

Shopify also has free chargeback protection — a fraud scoring tool — for eligible merchants. This allows US-based merchants selling physical products to get their chargeback fee and product value reimbursed. So long as it’s a fraud-related chargeback.

You lose money on the item’s value, but the dispute won’t contribute to your chargeback rate.

If you’re selling digital products, you won’t have much protection against fraud and chargebacks. Your best option is to consider an option like chargeback alerts. They notify you when a customer’s about to file a chargeback and give you a chance to refund them.

Integrating alert tools like Verifi with Shopify Payments could prove difficult without help. Using a certified reseller (like us) simplifies the process. In testing, I set up alerts in less than 5 minutes.

I’ve sold on Shopify for years (while using Payments) and always had a hard time getting a hold of their customer support. While this may vary by experience, keep it in mind if responsive support is a priority for you.

Shopify has a lot of fees, but they’re upfront about them. You shouldn’t encounter any hidden fees.

Fees

• Subscription: $5 – $2,300/mo.
• Chargeback fee: $15
• Payment processing: 2.9% + $0.30 – 2.7% + $0.00 (varies by subscription tier)

Accepted payment methods:

• * Google Pay doesn’t work for customers in France.
• ** Apple Pay is only available to merchants in the US, CA, AU, or NZ. Customers can only use it if they pay with Visa or Mastercard.

Let’s move onto a gateway that’s better for selling internationally.

2. PayPal: Best for International Transactions

Who should get it: Anyone selling physical products. Merchants looking to expand internationally.

Pros:

• Works alongside other gateways (e.g., Shopify Payments).
• Transparent about fees.
• Offers tools for small-to-medium-sized businesses.
• Responsive customer service (though results may vary).

Cons:

• Absurdly high chargeback fees.
• Not great for digital products.
• Limited payment options.

Number of merchants & transactions: “Tens of millions” of merchants use PayPal. It has processed $1.53 trillion in 2024 so far.

PayPal is excellent for international merchants, especially in Australia, the UK, and Canada. Since the gateway operating in over 200 countries and supporting 25 currencies.

One standout feature is PayPal’s "Pay Later" options, which help meet the growing demand for flexible payments.

A recent study showed that 40% of Buy Now, Pay Later (BNPL) users canceled or delayed their purchase when this option wasn’t available. That’s a huge opportunity to boost conversions.

Need more perks?

PayPal builds trust. They report that 74% of customers are more likely to buy from an unfamiliar store if PayPal is an option. This makes it an excellent tool for businesses looking to win over hesitant shoppers.

PayPal also shines when it comes to security. It offers real-time fraud detection and a Seller Protection Program. This program protects eligible transactions from fraud and delivery issues. Examples of purchases include those shipped to verified addresses.

Perfect for selling physical products.

Now, about customer service. My experience as a seller has been… mixed. Most of the time, the support was terrible — unhelpful staff, rude responses, and zero resolutions.

But other times? I met some of the nicest, most helpful people ever.

It’s hit or miss. But here’s the thing: they’re responsive. And that matters.

On chargebacks, PayPal has 2 processes.

One handles disputes made directly through PayPal (internal disputes). The other deals with chargebacks filed through cards, like Visa. If you’re going with PayPal, learn both processes. Chargebacks can sneak up on you.

Here’s an exceptional guide to teach you the basics.

If you sell digital products, though, PayPal doesn’t offer much protection. Consider using chargeback alerts to stay ahead of disputes. They warn you before a chargeback is filed, giving you time to refund and avoid penalties.

The good news? All chargeback resellers I’ve seen (including us) integrate seamlessly with PayPal.

Fees:

• Subscription: None
• Chargeback fee: All are non-refundable
  • Outside PayPal: $25
  • PayPal disputes: $8 – $16
• Payment processing: 3.49% + $0.49

Accepted payment methods:

You’ll have a hard time finding a processor as a high-risk merchant. What options do you have? Well. I did most of the research for you.

3. Authorize.net: Best for High-Risk Merchants

Who should get it: High-risk merchants in the United States, United Kingdom, Canada, Europe, and Australia.

Pros:

• Transaction fees aren’t too high.
• Accepts high-risk merchants.

Cons:

• Only available in select regions (US, CA, UK, EU, AU).
• Requires an additional subscription fee.
• Limited currency support.

Number of merchants & transactions: More than 430,000 sellers use Authorize.net. Processing $149 billion in payments yearly.

Authorize.net is a solid option for high-risk Shopify merchants in industries like supplements, travel, or digital services.

Authorize.net accepts almost any legal merchant. This means sellers in high-risk industries can use it without facing outrageous transaction fees. That’s rare for high-risk processors.

The platform also includes PCI DSS compliance. This protects sensitive data and helps meet legal requirements. In regions where PCI compliance is mandatory, non-compliance could result in heavy fines.

Most gateways already comply with PCI. Though, it’s reassuring to see this feature in a high-risk processor.

Now, here’s the catch: international purchases outside Europe and North America are tricky. 

Authorize.net only supports a handful of currencies:

Transaction fees are reasonable, but the subscription fee adds up. Combine that with Shopify’s costs and any premium plugins you’re using, and monthly expenses can get high.

If your business is high-risk because of frequent chargebacks, consider working on reducing those rates. You might be able to switch to a lower-risk (and cheaper) gateway.

We have a detailed guide on how to lower chargeback rates — it’s worth checking out.

Another downside:

Authorize.net doesn’t offer built-in chargeback insurance. You’ll need third-party solutions like Signifyd for fraud protection. This adds yet another subscription cost.

Fees

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

Accepted payment methods:

What if you’re not high-risk, but are dealing with recurring charges? You’re in luck.

4. Stripe: Best for Subscription-Based Services

Who should get it: Small-to-medium-sized businesses selling digital products. Thanks in part to its chargeback protection.

Pros:

• Automatically updates saved card details to reduce payment declines.
• Offers robust tools for merchants.
• Chargeback protection includes digital products.
• Supports over 135 currencies.

Cons:

• Chargeback protection is limited to US and European businesses.
• Only covers up to $25,000 in chargeback losses annually.

Number of merchants & transactions: More than 1.14 million websites use Stripe, processing around $1 trillion in 2023. That’s about 1% of the global GDP.

 Stripe is best for recurring payments due to its subscription management.

Features like automated billing and support for tiered or usage-based pricing let you design flexible plans for users. This helps reduce churn and improve retention. Key factors for subscription success.

Through Shopify, merchants can manage subscriptions directly from their store dashboard. Simplifying operations further.

Stripe Radar, Stripe’s fraud detection tool, is another highlight.

It has prevented more than 16.7 million fraudulent transactions while keeping false positives low. Blocking just 0.1% of legitimate payments.

Compare that to other fraud systems, which often reject 2 – 3% of valid transactions. Fewer false positives mean fewer lost sales and happier customers.

Stripe’s Chargeback Protection reduces these risks by covering eligible disputes (up to $25,000 annually) for a small fee. Unfortunately, this feature is only available to businesses in the US and Europe. It’s something to keep in mind if you operate outside those regions..

Stripe is built to scale with your business. Its infrastructure can handle high transaction volumes without slowing down. And with support for over 135 currencies, Stripe makes global expansion seamless.

Their currency conversion fees — while competitive — can add up. It’s worth reviewing their pricing for your target markets.

Fees

• Subscription: None
• Chargeback fee: $15; non-refundable
• Payment processing: 2.9% + 30¢ (Standard)
• Stripe Radar: $0.05 per screened transaction
• Chargeback protection: 0.4% per transaction
• 3D Secure: $0.03 per attempt

Accepted payment methods:

None of the above platforms allow you to accept cryptocurrency. Do any? Yup.

5. Coinbase Commerce: Best for Cryptocurrency

Who should get it: Anyone looking to accept cryptocurrency payments.

Pros:

• One of the most trusted crypto payment gateways.
• Immune to chargebacks.
• Low 1% transaction fee.

Cons:

• Cryptocurrency is volatile.
• Limited altcoin support.
• Managing crypto taxes is a nightmare.
• Coinbase has faced several controversies over the years.

Number of merchants & transactions: More than 8,000 sellers use Coinbase Commerce. They have processed over $200 million since its launch.

TL;DR: If you want to accept cryptocurrency, Coinbase Commerce is my top pick. I’ve personally used it. While the setup was frustrating, it worked without any issues once up and running.

This rest of this mini review dives into the nuances of using cryptocurrency for e-commerce.

Coinbase is a publicly traded company and is generally considered more reliable than other crypto gateways. However. Controversies around Coinbase (and crypto in general) make it hard to recommend any one platform.

Shopify offers several cryptocurrency gateways, including:

• Coinbase Commerce: Reliable but comes with its own controversies.
• Crypto.com Pay: Reportedly being probed by the Polish government for “unauthorized activities” [2].
• BitPay: Supports many altcoins.
• OpenNode: Only accepts Bitcoin.
• Bankful: Better suited for high-risk (legal) websites.

To set these up on Shopify, go to:

Settings > Payments > Additional payment methods (section) > Add payment gateway.

‍

From there, search “cryptocurrency.”

If you’re set on accepting crypto, it’s a case of choosing the lesser evil. But proceed with caution. 

Consult an accountant (not Reddit) before diving in. Managing crypto taxes can be a bureaucratic hell.

Cryptocurrency prices are volatile. Meaning the value of your earnings can drop before you convert it to fiat currency. If Bitcoin’s value falls after a transaction, you could lose money.

That said, crypto transactions are irreversible, which makes them immune to chargebacks. This can be a huge advantage for merchants. However. Coinbase advises merchants to issue “good faith refunds” if customers report fraud.

One major hurdle is crypto adoption.

As of 2022, cryptocurrency accounted for less than 0.2% of global e-commerce transactions [3]. But the trend is slowly growing. Around 16.1 million out of 41.2 million cryptocurrency holders used their tokens for online purchases.

Crypto is no longer just about buying illegal goods or two pizzas in 2010. But it’s still a small player in e-commerce.

This article is for informational purposes only. I, the author, do not endorse any specific cryptocurrency payment gateway, platform, or cryptocurrency. I presented all options based on objective research and analysis.

Fees

• Subscription: NA
• Chargeback fee: NA 
• Payment processing: 1%

Accepted payment methods:

If you’re a seller in India, you’ll have a hard time finding a gateway. Here’s what I found.

A Note to Sellers in India

Choosing a payment gateway in India is tricky due to regional restrictions.

Here’s what you need to know:

• Stripe: Supports domestic and international transactions. Though you must have a business registered as a Company, LLP, or Sole Proprietorship.
  • Individual merchants can only process payments within India—not from abroad.
• PayPal: Doesn’t process domestic transactions in India.
• Shopify Payments: Not available in India. Indian merchants must use third-party gateways to accept payments on Shopify.

Given these limitations, Razorpay stands out as a top option for Shopify store owners in India. It supports a wide range of local payment methods, including UPI, netbanking, wallets, and EMIs.

Razorpay also handles international transactions. Making it a great choice for businesses targeting domestic and global customers.

No matter which gateway you choose, take the time to ensure it fits your business needs.

Here’s How to Choose the Best Shopify Payment Gateway

Below is a quick breakdown of the key factors we’ve covered:

Each factor can affect how well a payment gateway fits your business goals. We’ll dive deeper to help you decide which gateway works best for you.

Let’s start with how gateways handle chargebacks.

1. How They Handle Chargebacks

Considerations:

• Chargeback protection
• Chargeback fees and whether they reimburse them
• Chargeback thresholds

Chargebacks can hurt your profits. Why? Because fees add up fast. Shopify Payments charges $15 per dispute, while PayPal charges up to $20. Some gateways refund these fees if you win the dispute, but many don’t. Be sure to check.

Does the gateway offer chargeback protection?

For example, Shopify’s Fraud Protection helps US merchants by covering disputes on eligible orders. However… Protections differ. If you’re in a high-risk industry, like digital goods, you may have limited options.

The dispute process matters too.

Can you handle disputes directly from the gateway’s dashboard? Or is the process complicated? Gateways with built-in tools for submitting evidence can save you time.

If chargebacks are common in your industry, choose a gateway with clear policies and protection plans. It’s not just about fees. It’s about keeping disputes simple and avoiding losses.

And preventing disputes. One way to do that is through fraud prevention.

2. Security & Compliance

Considerations:

• PCI compliance
• Data encryption
• Fraud detection

Your payment gateway must follow PCI DSS (Payment Card Industry Data Security Standard) compliance. Without it, you risk fines or legal trouble.

Encryption is another key feature. The gateway should protect transactions from start to finish, making customer data safe from breaches. Bonus points if the gateway uses tokenization. This perk converts card details into secure, unreadable data.

It’s like what Apple Pay does with its system. This has resulted in 25% fewer chargebacks for some sellers.

Fraud detection is essential for e-commerce. Many gateways use AI-powered tools to detect risky transactions. For example, Shopify Payments includes fraud analysis for free. Meanwhile, some competitors charge extra for similar features.

Security builds trust. Customers need to know their data is safe, and your gateway should make this easy for you and them.

Trust isn’t all that’ll get you paid. Choosing the best gateway is critical for budgeting.

3. Types of Payment Gateways

Considerations:

• Hosting model
• Integration complexity
• Control and customization

The type of gateway you choose impacts setup, flexibility, and user experience.

Here are the main types:

1. Hosted: Redirect customers to a third-party site for payments (e.g., PayPal).

• Best for: Small businesses needing a quick, secure setup.

2. API-hosted: Process payments directly on your site via APIs (e.g., Stripe).

• Best for: Businesses that want full control over the checkout experience.

3. Self-hosted: Store and process payments on your servers (e.g., Shopify Payments).

• Best for: Large businesses with the resources to manage security and compliance.

4. Local bank integrations: Connects directly to local banks for payments.

• Best for: Businesses targeting regions with specific banking preferences.

Each type has pros and cons. A list of which would make this guide too long. Match the gateway to your business needs.

Once you find a gateway, compare their fees.

4. Payment Processing Fees

Considerations:

• Transaction fees
• Currency conversion fees
• Payment method surcharges

Most gateways charge a percentage per transaction, but extra fees can sneak in.

Currency conversion fees are common if you sell internationally. These can range from 1 – 3% of the transaction amount. Some gateways, like Stripe or PayPal, also add cross-border transaction fees.

Different payment methods may have varying costs. For instance, credit card fees are typically higher than ACH bank transfers. Digital wallets like Apple Pay or Google Pay may also have separate fees.

Read the fine print. Make sure you know the total cost of processing payments. Especially if you rely on international sales or alternative payment methods.

These fees may also depend on where your customers live.

5. International Payment Options

Considerations:

• Supported currencies
• Local payment methods
• Cross-border fees

Planning to sell globally? Your gateway should support multiple currencies so customers can pay in their local money.

For example, European customers often prefer iDEAL. If your gateway doesn’t offer these, you might lose sales.

Again, watch out for cross-border fees. Many gateways charge extra for processing international transactions. For example, PayPal adds these fees on top of their regular rates.

Choose a gateway that supports international currencies. Also make sure it has local methods and clear fee structures. This reduces friction for global buyers and protects your profit margins.

Many gateways may have higher fees due to offering more features. You’ll need to find a balance.

6. Features

Considerations:

• Customization
• Multi-channel support
• Advanced reporting

Customization is key. Can the gateway integrate your branding into the checkout page? A seamless, on-brand flow improves trust and reduces cart abandonment. According to Baymard, 25% of shoppers in 2024 didn’t trust the site with their card information.

Branding, and proving yourself as a legitimate business, can help with this [4]. As it may show that you didn’t set up a Shopify account in a couple of hours and are trying to harvest user data.

Multi-channel support is another must. Your gateway should work across websites, marketplaces, and in-person sales if you use POS systems. Integration with platforms like Shopify, Amazon, or Etsy can streamline operations.

Advanced reporting tools help track sales trends and customer behavior. For example, analyzing Average Transaction Value (ATV) can reveal opportunities to boost revenue.

Choose a gateway that supports your needs now and can grow with your business later.

You could consider payment methods as a “feature” as well.

7. Accepted Payment Methods

Credit and debit cards remain staples, but their dominance is fading. Digital wallets like Apple Pay and Google Pay now account for over 50% of global e-commerce transactions. Thanks to their speed and convenience.

If your gateway doesn’t support these, you could miss out on sales.

Buy now, pay later (BNPL) solutions are booming, particularly with younger shoppers. By 2025, they’re expected to handle nearly $700 billion in global transactions. Services like Afterpay and Klarna make large purchases more accessible. Reducing sticker shock and boosting average order values.

Think globally, too.

Different regions prefer different methods. For instance, Alipay is dominant in China. Meanwhile, Europe may lean on bank transfers like SEPA. Choose a gateway that supports your audience’s preferred methods, ensuring every shopper has a way to pay.

Your customers can’t pay if the gateway isn’t functional. Here’s what to consider in that area.

8. Reputation & Reliability

Considerations:

• Uptime and stability
• Customer support
• User reviews

A payment gateway’s reputation can make or break your operations. Uptime is critical — downtime means lost sales. Look for gateways boasting 99.9% uptime.

During my research, all gateways claimed to have this uptime.

Reliability extends to customer support. Does the provider offer 24/7 help? Quick response times? When payments fail or systems glitch, fast support minimizes disruption. Gateways like Stripe are known for robust support systems, but others may lag behind.

Check user reviews.

Do merchants praise the gateway for ease of use and reliability? Or do they report hidden fees and delays? Researching this upfront can save you headaches later.

A reliable gateway means smoother operations, happier customers, and fewer surprises.

We’re just about done.

Wrapping Up

Shopify supports hundreds of payment gateways, and this guide only scratched the surface. For more options, check out our full guide on the best Shopify Payments alternatives.

No matter which gateway you choose, chargebacks will cause issues at some point. High chargeback rates can cost you money — or even your business.

Want help managing chargebacks? Tools like chargeback alerts can make a big difference. We offer alerts that integrate seamlessly with many popular gateways.

Try them today.

Sources

• [1] Ecommerce stores using Shop Pay. Store Leads. 11/22/2024
• [2] Poland Probes Crypto.com. Finance Magnates. 08/11/2024.
• [3] Crypto payments – statistics. Statista. 2/29/2024.
• [4] Cart Abandonment Rate. Baymard Institute. 2024.