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Best Payment Gateway Processors for Ecommerce Stores

Branko Mijatovic Updated on March 29, 2020

payment gateway

With ecommerce sales projected to hit $632 billion by 2020, it’s no wonder ecommerce is one of the fastest growing areas for first-time entrepreneurs.

Whether you are an existing ecommerce business owner or you are planning to open your own store, you have probably had it drilled into you that “you need to build a list” or “you need to make sure you have an autoresponder.” Yet one of the key areas that is often overlooked is how you are going to collect payments from the customers who shop on your online store.

The sheer number of payment gateways out there (and the different features they offer) can make it confusing, if not completely overwhelming, for an ecommerce business owner — especially if you are starting out.

Here is what you need to know when choosing a payment gateway: our list of the top five providers, along with their pros and cons, in order to help narrow down the options and cut through the noise.

Does it work with my ecommerce platform?

What gateway you can use really depends on how you are selling your products online. If you already have an established store and you are considering changing your existing provider for a better deal, you are going to have to work out what gateways your current store supports.

Most of the big hosted ecommerce platforms support a majority of payment gateways. But if you have a custom self-hosted solution, you may come up against some limitations.

If you are new to ecommerce, it’s more than likely you are going to start out with something simple like Shopify. Platforms like this have a bunch of pre-existing integrations, along with support for many more if you choose to change later on. This is great because you can get selling as soon as possible with almost no setup time.

Also, most of the big platforms allow you to integrate different payment gateways for no additional charge. For example, if you use Shopify to host your ecommerce site, you can choose from over 70 gateway providers. BigCommerce supports over 40 integrated solutions. However, if you want to add a specific payment gateway to WooCommerce (a WordPress-based ecommerce solution), you may have to pay an additional fee for the necessary plugins.

How secure is it?

When taking payments online and handling customers’ personal information, security becomes a big concern. Not only is there the risk of loss of revenue from fraud, but if you mishandle personal data, the penalties can be so high that they can destroy your business.

Anyone who is in the business of collecting or storing card data has a requirement to be PCI compliant. While your payment provider is required to handle and store data according to PCI standards, you have to make sure that when your store is sending data to and from your provider, you handle it securely.

The way to make sure the connection between you, your customer, and your payment gateway is secure is to have an SSL certificate. The SSL encrypts the transmission of payment data between your store and your payment provider to protect against a man-in-the-middle attack — where a hacker could fool you into thinking their computer is your server and steal customer credit card information.

If you are running an already-hosted ecommerce store like Shopify or BigCommerce, then PCI compliance shouldn’t be an issue, as platforms like Shopify include a free SSL in their plans. However, if you are running a store that is hosted on your own servers, then you need to make sure you are PCI compliant; otherwise, you risk opening yourself up to liability.

Your hosting provider will usually have a number of SSL security certificates that are available for purchase, with varying degrees of protection. However, they are typically more expensive than if you purchase them from a third-party SSL provider such as Namecheap.

There are a ton of options with SSLs, so you may need to spend a bit more time researching what is suitable for you.

How much is it going to cost me?

When choosing your provider, it’s important to choose the right one for your business and for what you are trying to achieve. Some providers provide a higher per-transaction fee but they don’t require any subscriptions. Others give you lower overall transaction costs but they require a monthly subscription payment and a setup fee to use the system.

If you are running a high-volume ecommerce business, it may make more sense for you to pay a flat monthly fee and take advantage of the lower transaction charges. Whichever option you choose, make sure you sit down and run some numbers so you can ensure you are getting the best possible solution for your ecommerce business.

If you are running an international business and charge in multiple currencies, you need to make sure that your provider doesn’t sting you with any additional fees for international payments or currency conversion. These fees can be really bad for business if you are running an operation with tight margins and can mean the difference between making a profit or losing money on each sale.

Let’s take a look at the top payment gateway providers.

5 Popular Payment Gateway Providers

So, you’ve set up your site, checked what payment gateways are supported, and have an SSL certificate in place to ensure you are PCI compliant. So how do you choose a gateway provider? While there are countless payment gateways in the market today, all provide different levels of service, options, security, and charges.

These are, by far, the largest and most popular gateways on the market:


If you’ve ever purchased anything on the internet, you’ve probably heard of PayPal. It was the first company to provide a way for money to be easily and securely paid and transferred over the internet without the need for a credit card. The ease of use and simplicity of setting up a PayPal system makes it a typical first choice for many entrepreneurs.

However, this simplicity does have some downsides. While their fees are competitive with the country in which you typically do business (e.g., U.S. PayPal account and a customer purchases a product using a U.S. credit card) — when taking payments from international cards, you get slammed. A rate of 4.4 percent is charged for international credit cards. plus a transaction fee, and to top it off, PayPal’s currency conversion rates are some of the worst on the market. Further, there have been regular reports of people’s accounts being frozen (along with any funds inside) with no warning or justification, which can greatly impact your ability to purchase more stock for your business.

However, with over 218 million users, PayPal is a massive platform; many potential customers have PayPal accounts, making PayPal pretty hard to ignore.


  • A 2.9 percent charge plus $0.30 fee per transaction (with an option for volume discounts)
  • PayPal Express does not have a monthly fee and you can cancel at any time
  • Supports all ecommerce platforms using PayPal’s redirection to their site
  • PayPal Express integration allows direct payment on your site using the PayPal Express application programming interface (API)


  • Known to freeze accounts and funds with little or no warning
  • Payment add-ons, such as fraud protection and recurring payments, cost extra per month
  • A 4.4 percent charge plus a fixed fee per international transaction
  • Terrible currency conversion rates
  • If you don’t want the PayPal button, you will need a PayPal Pro account at $30 per month
  • A $20 chargeback fee


Stripe is a payment processor whose motto is “developers first,” which is why Stripe is a favorite among developers and ecommerce owners running custom-built ecommerce stores.

However, aside from their development roots, they are great for non-technical people, with easy-to-setup API integrations for all the major ecommerce platforms. And with reasonable fees, Stripe is one of the most popular payment providers for online retailers.

Stripe is, by far, the most innovative payment processor — with a development focus, they are continually improving and adding new functionality such as Bitcoin payments and, more recently, their beta test for WeChat Pay. This constant innovation gives online retailers the opportunity to tap into markets that other payment processors do not currently support while knowing any upcoming technologies will likely be implemented in the future.


  • Easily integrates with BigCommerce, Shopify, WooCommerce, Magento, and Spree Commerce
  • API for integration with custom solutions
  • A 2.9 percent charge plus a $0.30 transaction fee
  • A $15 chargeback fee
  • No contract requirements
  • No additional charges for recurring payments
  • Supports Automated Clearing House transfers, Alipay, and Bitcoin (WeChat Pay in private beta)


  • Extra 1 percent charged on international card purchases


Authorize.Net has been around a long time and has managed to maintain a decent foothold in the payment gateway space. It is compatible with most big ecommerce platforms and offers features like fraud protection, subscription payments, and their simple checkout for no extra charge.

If your business gets big enough where you opt for a merchant account with your bank in order to get better fees, Authorize.Net offers a Payment Gateway Only plan so you don’t have to change anything on your site. However, this flexibility comes with a price; to use Authorize.Net’s platform, you will need to pay an initial setup fee and a monthly subscription.

Authorize.Net also does not allow the ability to transfer your customer card data if you were to ever change to a different payment gateway, unlike their competitors such as Stripe and Braintree, which allow you to transfer data in a PCI-compliant way. This could be a big issue if you have a lot of customers and deal with recurring payments.


  • Integrates with the big name platforms: BigCommerce, Shopify, Volusion, WordPress, and Magento
  • A 2.9 percent charge plus a $0.30 transaction fee
  • Provides secure customer data management for managing your customers’ private information
  • Syncs with QuickBooks if you are using the QuickBooks accounting software
  • Payment Gateway Only option available if you have a merchant account with your bank


  • A $49 setup fee
  • Charges a $25 monthly gateway fee
  • A $25 chargeback fee
  • A 1.5 percent additional fee for international transactions
  • No way to migrate customer data if you ever have to change your payment gateway


Braintree rose to stardom since its launch in 2010 as a competitive payment gateway alternative. Even though Braintree was acquired by PayPal, they have still managed to maintain their competitive rates.

One of the major positives of Braintree is that it accepts PayPal, Apple Pay, Android Pay, Venmo, and even Bitcoin (through Coinbase). But the lack of official support for Shopify could be a deal breaker for many ecommerce business owners.

If you have customers who pay using one of the many payment options Braintree supports, and you don’t use Shopify for your online store, then Braintree may be a suitable option for you.


  • Supports major platforms: BigCommerce, Magento, Spree Commerce, WooCommerce
  • A 2.9 percent charge plus a $0.30 transaction fee
  • A $15 chargeback fee
  • Accepts payments from PayPal, Apple Pay, Android Pay, Venmo, and even Bitcoin.


  • No Shopify support
  • Charges a 1 percent additional fee for international payments
  • PayPal payments still subject to the standard PayPal fees

Amazon Payments

Amazon launched their payments service in 2007. Their goal was to give customers the same shopping experience they receive from Amazon on third-party sites. Just like with Stripe and PayPal Express, the customer can conduct their purchase through Amazon’s payments system without ever leaving your site.

The big benefit for your ecommerce store is the ability for customers to access their one-click shopping options, which makes it even easier for customers to shop on your store. It also means customers can use their stored shipping and payment information that is on Amazon’s servers. They simply log in with their Amazon account and their payment data and shipping information are seamlessly transferred to your site — saving both you and your customers time. And with competitive rates, it’s a great alternative to PayPal.


  • Supports Magento, Shopify, WooCommerce, Volusion, and BigCommerce
  • A 2.9 percent charge plus a $0.30 fee per transaction
  • No setup fee
  • No fraud protection fees
  • No contract


  • A $20 chargeback fee

Choose Wisely

There you have it: a quick run-through of what you should look for in a payment processor and several popular solutions for online retailers.

If you are just getting started, using some of the built-in integrations provided by your ecommerce platform will work just fine. But if you are looking to scale up or get a better deal on transaction fees, then you should shop around and get the best deal for your business.

Whatever may be your situation, it is still recommended that you do your own thorough research before deciding what is best for you and your business.

Photo credit: AlexLipa

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