Shopify Payment Gateways: Which One Fits Your Business Best?

November 28, 2022 Julio Romero

Reading time about 14min

Shopify Payment Gateways: Which One Fits Your Business Best?

Jairene Cruz-Eusebio on Nov 3, 2021 4:00:00 PM

Payments are an essential aspect of any business. The reason anyone would start a business is to make profits, after all! And if you have moved your business online, one of the first things you should look into is how to accept payments over the internet.

If you’re on Shopify and are current on the lookout for a reliable payment gateway for your online store, then you’re in the right place! We’ve done the work for you by reviewing five of the most popular Shopify payment gateways in detail so that you can make an informed decision when choosing one for your store.

Table of Contents

How to Choose a Shopify Payment Gateway

7 Best Shopify Payment Gateways

1. Shopify Payments

2. Stripe

3. PayPal

4. Authorize.Net

5. Alipay Global

6. Skrill

7. Opayo

Payment gateways were developed to create a more reliable and smoother way for business owners to receive payment. You can think of a payment gateway as your cashier that allows various electronic payments from customers.

As the name implies, Shopify payment gateways are payment portals made specifically for or by Shopify. It simplifies the process allowing users to make payments securely through different means—via bank transfer, credit card payment, e-wallets, and more.

You can’t have a complete Shopify business without using a payment gateway. Not only do they enable transactions by moving information between two different portals (from the website to payment processors like banks), but they also securely transfer the customer’s payment details to the bank and receive a confirmation about the accepted or declined transaction.

But before we begin discussing the best payment gateways available, let’s first discuss how you can narrow down your options.


How to Choose a Shopify Payment Gateway

Choosing the right payment gateway for your business is challenging. Shopify has dozens of gateways, and there’s no way you can do thorough research on them all. You need to look at reviews and ratings, but every review is different, and most people don’t write reviews about their bad experiences with any particular gateway. And even if they did, how many negative reviews would it take before you decided that this might not be the best option?

So when deciding on your best option, you should consider the following first:

1. Local and Global Availability

Your ideal payment gateway should match your business goals. Perhaps this is the most important factor to consider before choosing any payment gateways: always have a clear idea of the maturity of your business.

Ask yourself: do I intend to remain local, or do I aspire to go global?

Why is this important? Well, if you plan on going global, your payment gateway should be able to fulfill your needs when the time comes. You don’t want to have to look for a new payment gateway the moment you decide to expand—it should be the least of your worries.

Will your payment gateway of choice be able to accept payments from other countries where you plan on expanding to? Will changing currencies between your home country and your international market have any effect on the processing of payments?

2. Affordability based on Accumulated Fees

It’s not enough to like the services a payment gateway offers. How expensive a payment gateway is will determine the amount of profit you’ll get and the price of your products. If you ignore the costs, it will be bad for your business.

Also, note the frequency of payment. Some payment gateways may charge monthly, so be sure to put this into consideration.

Other fees like statement fees, chargeback fees, and cancellation fees are other factors you should consider before choosing a payment gateway. Here are some fees you should look into before signing up with a payment gateway:

  • Transaction or Processing fee – This can either be a fixed price per transaction or a percentage of the transaction amount.
  • Anticipation fee – This is the fee charged for cases where you want to receive the money before the actual payment is deducted from the buyer. Take, for example, during installments. If you get full payment of the product that is paid for in installments in the buyer’s credit card, you will be charged the Anticipation Fee. Not all banks and payment gateways charge this.
  • Annual fee – This is the payment gateway’s service fee charged on a yearly basis. This is charged on you whether or not you received any payment through this gateway throughout the year.
  • Monthly fee – This is similar to the annual fee, except this one is charged monthly. This can be based on the transactions performed on the payment gateway, or it can also be a fixed price.
  • Minimum monthly fee – This is the amount you need to pay regardless of the number of transactions you had.
  • Refund fee – This is the amount you have to pay the processor when a refund to a buyer is made.
  • Settlement fee – This is the amount you pay for transferring the collected revenue to your bank account.
  • Currency conversion fee – This is the amount payment gateways charge for changing payment currency to your local currency.

Keep in mind that this is not an exhaustive list. Some payment gateways have other fees specific to their processes, so make sure you double-check.

Also, different gateways charge differently. For instance, PayPal and Stripe both do not charge a refund fee, but the processing fee you paid during the initial transaction will not be sent back to you.

3. Accepts Multiple Payment Types

multiple payment options

It is essential to know which payment types a payment gateway can accept before committing yourself to use them. Do they also accept debit cards, prepaid cards, gift cards, and e-wallets?

Is there a difference in fee or processing if the customer uses a payment option other than a credit card?

For instance, some payment gateways charge more when they process debit cards compared to credit cards, even though both charges come out as percentage-based fees. So make sure whichever payment method you choose, it has the best rates possible regardless of what kind of transaction it is (credit or debit).

4. Accepts Multiple Card Brands

It is advisable to go with a payment gateway that allows the acceptance of all major payment types. This way, you can avoid making your customers pay extra just because your payment gateways don’t accept their preferred card. You can also avoid losing customers who do not have cards that match what your gateway can accept.

This also applies to international transactions since payment gateways vary from country to country. You’ll also want to check whether your payment gateway can accept cards issued internationally.

5. Settlement Schedule and Currency

This is where payment gateways need to be transparent and clear in their policies. Some payment gateways send funds instantly to your connected e-wallet or bank account, while others deposit your funds on a set schedule of the month (such as 15th or 30th).

Knowing when you’ll receive funds allows you to manage your business’ cash flow properly.

Furthermore, you should know if your payment gateway will convert the money into your country’s currency before it gets deposited into your bank account, especially if you’re accepting international orders. And when they do convert the currency, how much do they charge?

Some payment gateways don’t charge for settling your funds (depositing the money to your account), but when they convert the currency, they get a percentage of the conversion (called the Currency Conversion Fee).

6. Has a Good Reputation

When choosing payment gateways, you need to know which payment service providers have been in the market for several years. This way, it is easier for you to trust their processing system and what they’re offering because if this payment gateway has been in business long enough in your country or continent, then there must be some truth behind its legitimacy.

After all, no reputable company wants to ruin its reputation due to poor management (which includes bad customer reviews). So when considering payment gateways, do not risk your eCommerce store by using new payment processors with hardly any feedback about them unless you’re willing to test out whether these payment processors will work well with Shopify’s platform.

7. Fraud Payment Detection

After choosing which payment types are accepted by the payment processor, next is checking on its features that allow it to stand out among the rest in terms of security measures that protect both you and your customers while processing payments online.

Fraud payment prevention helps you avoid chargebacks that can accumulate in your business’s cash flow and even put you on the edge of bankruptcy if it isn’t handled well. To be honest, this is one area where payment gateways need to improve their services since some do not have an effective system for detecting fraudulent transactions that they’ll just push through anyway (even when there’s a high risk).

8. Solid Customer Support

Last but not least, payment gateways should have a solid customer support team that aims to provide solutions as soon as possible. In case you encounter problems with your payment gateway or have questions about its policies, then it is best if they can answer those inquiries immediately instead of leaving customers waiting for days on end.

After all, every business needs a payment gateway that will make them feel like they’re part of their family because this payment processor cares more about your eCommerce store’s growth and prosperity rather than just making money from commissions.


The right payment gateway is where you receive excellent services at an affordable price no matter how big (or small) your eCommerce store becomes! If it seems that the payment processor will only treat you well if you’re a big business, then you’re better off working with those who value you even when you’re just starting out.


7 Best Shopify Payment Gateways

These payment gateways should help you get a bigger piece of this eCommerce pie because they have been in the market for several years and have solid reputations.

Let’s explore the top seven best payment gateways currently available, as well as their benefits and drawbacks.


1. Shopify Payments

Shopify Payments is a payment gateway designed and built by Shopify to help entrepreneurs grow their eCommerce businesses. This payment processor accepts all major credit cards (Visa, MasterCard, American Express) as well as PayPal, which is a plus for many online business owners who want to accept not just one but multiple payment types when selling products or services on their Shopify store.

The biggest drawback of choosing this payment processor is that your funds can be frozen without warning when they detect suspicious account activity.

How to Setup Shopify Payments

First off, you need to know if your country is accepted. If it is, make sure the products you are selling or services you are offering are allowed under Shopify Payments Requirements.

In order to set up Shopify Payments, follow the steps on this page. Keep in mind that verification regarding your business and personal information will be done before Shopify Payments is activated.

Shopify Payments Pros:

  • Solid security measures
  • Accept payment through PayPal

Shopify Payments Cons:

  • Available only from merchants from a handful of countries
  • High chargeback fees of up to $15 per event
  • Sudden freezing of funds when suspicious activity is detected


2. Stripe

Stripe is a payment processor that has been in the eCommerce industry for twelve years now. This payment gateway accepts all major credit cards (Visa, MasterCard, American Express) as well as Apple Pay which makes it easy to accept payment from customers regardless of what country they are located in.

The only drawback with Stripe is its high transaction fees (2.9% plus 30 cents), currency conversion cost, and more. This is especially problematic for businesses selling low-priced products. Even more so for those accepting payments through mobile devices because these transactions have additional charges.

You may notice that Stripe rates and Shopify rates are almost the same. The reason for this is simple; it’s because Stripe is actually the payment gateway behind Shopify Payments.

If so, why would you bother using Stripe instead of Shopify Payments? The simple explanation for that is because Stripe has better customer service than Shopify Payments.

How to Set Up Stripe Payments in Shopify

First thing’s first, make sure that your country is included in the list of countries where Stripe payment gateway is available. If not, you can always try another payment gateway to see if it will work for you.

Next, make sure that the products or services you are selling or offering on your Shopify store are allowed on this payment processor. For example, if you’re from the US and trying to sell a car on your eCommerce store, Stripe payment gateway would reject it because it takes a stricter approach with what products or services can be sold on Shopify stores.

To set up a Stripe payment gateway on Shopify, follow these steps:

  • Visit your Shopify admin panel
  • Go to Settings > Payment providers (tab) and click on the “Enable payment method” button under the Stripe payment gateway.
  • Enter your payment information such as merchant ID, Shopify API key, and save it.

And that’s all! Stripe payment gateway is now enabled in the payment providers section of your Shopify admin panel. You can start accepting payments from customers right away.

Stripe Payment Pros:

  • Solid security measures
  • Accepts more than a hundred currencies
  • Extra features include mobile payments, one-click checkouts, and subscription billing.

Stripe Payment Cons:

  • Similar to Shopify Payments, accounts can be put on hold without warning, and additional documentation will be required to reactivate the account. Since they have better customer service, though, it only takes a day or two at most to get the funds unfrozen once complete documents have been submitted.


3. PayPal

PayPal is a payment processor that allows you to accept payments from customers through the use of credit cards, debit cards, or eWallet. It also offers international payment methods such as bank transfers and local payment options for around 200 countries worldwide which easily makes it one of the most versatile payment gateways in its industry.

The only setback with PayPal is that it does not offer as many payment options and features as Stripe, but if you’re just starting out and your eCommerce store is still new, we would recommend using PayPal.

The good news is that you will not be double-billed when using Paypal in Shopify. Shopify payment gateway will only be used to process the payment and any fees associated with Shopify’s services.

How to Set Up PayPal on Shopify

By default, Paypal Express Checkout is enabled in every Shopify store. The email associated with Paypal will be the email used to create the store. If you or your business already has a Paypal account using a different email, you can change the account.

You can simply go to the payments page of your Shopify Store, then active Paypal Express Checkout.

Paypal Pros:

  • One of the biggest payment gateways in terms of payment options and payment locations
  • Relatively low transaction fees compared to other payment providers.

Paypal Cons:

  • Currency conversion fees are high. They don’t indicate how much, but you will notice the big difference between the actual conversion rate and what Paypal offers.
  • The Paypal Express Checkout button confuses customers, leading people to believe that Paypal is the only payment option available.
  • The shipping information is skipped. Hence users don’t pay for the correct shipping fee.


4. Authorize.Net

Authorize.Net payment gateway is one of the most popular payment methods for eCommerce stores as it was designed primarily with online businesses in mind. This payment processor provides a secure and reliable payment service that can easily integrate into your Shopify store’s checkout process, allowing you to accept credit card payments from customers worldwide without hassle or added costs. charges a monthly gateway subscription fee of $25, plus transaction fees of 2.9% + 30¢.

How to Setup on Shopify

To set up the Authorize.Net payment gateway on Shopify, you will have to sign-up directly from your eCommerce store’s dashboard as it is not enabled by default with the platform.

To link your Authorize account to your Shopify store, you would need the API and transaction key credentials from the former. Pros:

  • It is a popular payment processor for US-based online businesses.
  • It also accepts e-wallet payments such as Paypal and Apple Pay, as well as e-checks. Cons:

  • Relatively high transaction rates compared to other payment gateways such as PayPal and Stripe (what with monthly subscription fees plus transaction fees).
  • Business must be based in the US, UK, CA, Europe or Australia.


5. Alipay Global

Alipay is a payment service provider which provides online payment solutions for eCommerce businesses. It was launched in 2004 and has since been the preferred payment method for Chinese buyers all over the world, which makes this payment gateway a good choice if they are part of your target market.

In 2016, Alibaba Group partnered with First Data Corporation to launch Alipay Global (formerly known as Alipay), enabling international merchants to accept payments from customers who use this payment gateway on their Shopify stores.

The great thing about using an international payment solution such as Alipay Global is that it doesn’t matter what country you are selling your products or services to—if they can access your Shopify store through any internet browser, then they will be able to make purchases using the selected payment methods available under this platform.

How to Setup Alipay Global on Shopify

Setting up Alipay payment gateway on your Shopify store is pretty straightforward. You just need to choose Alternative Payment Methods under Payment Settings and look for Alipay.

Once you click on the Connect button, an Alipay sign-up form will open up. You can go ahead and register if you still don’t have an Alipay business account. Make sure you complete your business details and upload your registration certificate from your country if you want to be approved without a hitch.

Alipay Pros:

  • A popular payment method used internationally and preferred over other methods.
  • Accepted worldwide and supports 14 currencies.

Alipay Cons:

  • You must be running an eCommerce business with a physical presence in one of these countries—the US, Australia, China, France, Germany, Hong Kong S.A.R., Italy, Japan, Netherlands, and the UK; online stores need to have their own domain name for verification purposes (this can’t just be a subdomain or shared hosting).
  • Alipay Global has a monthly subscription fee of $79. Transaction fees are said to start at 0.55%, but the rate depends on the merchant account. The merchant must first apply to have an account before seeing the actual fees.


6. Skrill

Skrill payment gateway is one of the world’s preferred eCommerce payment methods, catering to millions of online shops and retail chains worldwide. This payment option enables businesses to accept payments from customers using their credit cards or bank accounts without having to worry about fraud detection as Skrill has you covered with its built-in security features.

The best thing about choosing this payment method for your Shopify store is that it doesn’t matter what country your business operates in – if the customer wants to pay by their card, Skrill will facilitate electronic transfer through an internationally recognized banking network that makes international transactions quick and convenient.

Skrill accepts Visa, Mastercard, Maestro, Klarna, Giropay, and Neteller.

How To Setup Skrill On Shopify:

To use Skrill on Shopify, you must first create your account in Skrill and configure your API Password and secret word. It requires a bit of know-how, which is why Skrill created this module on how to link their platform to Shopify.

When you’ve finished the instructions in the module mentioned above, then you can come back to Shopify and add Skrill through the Alternative Payment Methods page.

Skrill Pros:

  • This payment gateway has one of the lowest transaction fees, at 1.2% plus EUR 0.29. That is roughly half of what most of the payment gateways mentioned above charge.
  • Supports at least 40 currencies worldwide.
  • More than 100 payment options, including credit card, debit card, e-wallets, and bank transfer.

Skrill Cons:

  • Withdrawal fee of EUR 4.00 per event. So if you want to reduce withdrawal fees, you might as well schedule your withdrawals when there are enough funds.
  • High Currency Conversion fee of 3.99%


7. Opayo

Opayo, formerly known as Sage Pay, is one of the most popular payment gateways in the UK. It is used by more than 50,000 online payment merchants and has a clientele in around 180 countries.

Opayo is very simple to set up on your Shopify store with minimal steps involved. You can make international transactions without worrying about cross-border fees or conversion rates because Opayo offers its services at the same price regardless of where you’re receiving payment from.

This payment gateway has three subscription levels. The Flex Plan costs £25 a month for 350 transactions; the Plus Plan costs £45 a month for 500 transactions; the Corporate account has bespoke pricing and is meant for businesses with at least 3,000 transactions a month.

In short, you pay a fixed monthly fee regardless of whether you reach your transactions limit or not. You will, of course, be charged extra if your transactions go over the monthly limit, but this price is still significantly less than most payment gateways. Plus, it doesn’t matter how much the total order cost is!

How to Setup Opayo on Shopify

Opayo can be linked to Shopify via the Alternative Payments page. Once you see Opayo, click on Connect, and you will be asked to sign up. While signing up is easy, activation and approval can actually take a month.

You can also link your Opayo account (if you already have one) to Shopify via Wallee integration.

Opayo Pros:

  • Fixed monthly payment with no additional fees per transaction.
  • Highly competent fraud detection technology

Opayo Cons:

  • Approval takes a while because this payment gateway is very thorough when it comes to investigating merchant backgrounds.

Final Thoughts on Choosing Payment Gateways for Shopify

Whichever payment gateway you choose for your Shopify store, there are some factors to consider.

Is it easy to set up? If the payment gateway is difficult to integrate with your Shopify account, then this may end up being a headache that takes too long and will cost more time in lost revenue.

Which payment methods does it support? Check whether or not the payment method suits your target audience before committing because if they don’t use that type of payment method, then expect fewer conversions—which means fewer profits for your business!

How secure is it? What kind of fraud detection technology do they have in place? Do they offer customer service 24/7 so if anything goes wrong, you can address their team immediately without getting in the way of your business growth?

Is it affordable? There are payment gateways with low fees and payment gateways where you pay a little more for added security. It is up to your budget in the end but you should know that if their prices seem too good to be true, they probably are!

Finally, is it something that your customers trust? Because if your own customers don’t trust them to process their payments or to handle their sensitive financial information, then all this is moot and academic! A trustworthy payment gateway helps customers trust your business as well.

While choosing a payment gateway is an essential aspect of building your online store, don’t take too long to choose! This should not be a bottleneck when taking your business online—instead, it should help ease your burden when it comes to accepting payments.

Once you’ve chosen a payment gateway, the next step is to choose Shopify marketing apps that can help boost sales! One that we highly recommend is WinBack, an SMS Marketing app that can help recover a third of your lost sales. Try our 14-day free trial and see how it can instantly help your business grow.


Topics: Shopify Marketing