Best payment systems for e-commerce

Best payment systems for e-commerce

After Covid-19 outbreaks and the following lockdowns, most businesses had to shift to and focus more on e-commerce. Undoubtedly, it was not the only reason for moving most of the sales online. During the past decade, the tendency for purchasing and buying all goods and services online has been only increasing. As most stores (except for the grocery ones) were closed all over the world during lockdowns, it only resulted in a push for all the companies to concentrate on online orders and sales, accordingly. 

Every business that operates online needs an efficient payment system. The question is: how do you pick one? What features should you look for when selecting an e-commerce online payment solution and what’s the average pricing? All these questions and more Genome‘s answering below. 

What is an online payment system?

To put it simply, an online payment solution is a set of tools that merchants use to accept online payments on their websites. In this article, we’ll focus on one of the central elements of such systems – payment gateways. We will also talk a little bit about the online payment system as a whole to provide the full picture. 

First of all, let’s have a look at all the elements of the payment solution and what their roles are: 

Merchant account

If you’re already involved in e-commerce or only planning to open an online store, you’ve probably heard about the merchant account. It allows you to accept payments from your online store. All transactions and funds you earn due to online transactions made by your customers settle in your merchant account. Only then, you can move these funds to your business bank account. 

With Genome, merchant accounts come for free if you’re opening a business account with us. All you need to do is register on our website, provide the required information, and upload the necessary documents. Apply online and start trading online as soon as possible. 


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Payment gateway

The next crucial tool for e-commerce is the payment gateway. PG enables card payments on the merchant’s website. It saves and encrypts data from the bank cards of your buyers during the checkout. The window to fill in card details is a visual representation of the payment gateway technology. After PG receives card details, it checks whether the card is valid and passes the information further. For merchants, just like for buyers, a payment gateway means additional security and protection from fraudsters (who can use fake or invalid bank cards).  

Payment processor

Last but not least, let’s talk about payment processors. They are also known as payment service providers (PSP) or payment facilitators. The payment processor receives a transfer request right after the payment gateway finishes card verification. Then, a PSP sends the inquiry to a particular card association (Visa, Mastercard, etc.). Card association, in turn, contacts a card-issuing bank to move funds from the owner’s account to the merchant’s account. If the bank approves a transaction, a buyer receives notification that they were charged and vice versa. And all this happens in less than one minute. 

How to choose an e-commerce online payment solution?

As every business is different, an optimal e-commerce online payment system will also differ depending on many factors. Here are the most important things to pay attention to: 

Hosted vs integrated PGs

Integrated payment gateways work with the help of provided API (application programming interface). It means that even when the customer fills in their card details, they stay on the merchant’s website. If you’re not a tech-savvy person, you will probably need somebody to install this API for you. Additionally, such a service may cost higher for using API. 

Hosted PGs redirect clients to the payment processor’s website at the moment when card details are needed. Unlike integrated payment gateways, hosted ones are pretty easy to set up. 


Remember that PGs have access to your client’s data. That is why you should make sure that this information will be properly protected. To accept card payments, your best payment gateway has to be PCI DSS compliant (Payment Card Industry Data Security Standard). 

Data portability

You need to know how to download and move your customers’ data. For example, if you want to shift to another PG, you would have to retain all the information. 

Different payment methods

Card payments are probably the most popular ones when it comes to online shopping. Nevertheless, with every year there appear more and more new transaction types. For example, now your clients can pay with digital wallets or Apple/Google Pay. Learn more about your potential customers and what payment options they prefer. In such a way, you will be able to select a payment system that supports the necessary transactions. 

Cards accepted

The most common card associations are Visa and Mastercard. However, if you’re working with American customers, your website has to support American Express cards too because they are widely spread in the US. The fees for processing different card payments also vary. 

Mobile optimization

More and more people use smartphones for online purchases instead of laptops or computers simply because it’s more convenient, faster, and effortless. No wonder that your online payment solution has to work perfectly well on all types of devices. If a payment gateway is not optimized to work with smartphones, you may lose plenty of clients because they will find a merchant whom they can pay from their mobile phones. 

User experience

Your customers’ journey is crucial on all levels: beginning with how easy your website is for navigation and ending up with how fast they can checkout. Undoubtedly, it also includes their experience with payment gateways and processors. Choose a payment system that will be intuitive and not too complicated. If your clients cannot find the blank spaces or some buttons to finish their transaction, they will likely not only give up on your goods/services but will probably never come back to do another try. 


Charges vary from PG to PG. It’s quite common to charge a flat fee for every transaction plus some percentage based on the average sum of your payments. Moreover, there are also different fees for credit and debit card transactions, as well as for international transfers. If you want to stick with the best online payment system with low rates, you should first get to know your clients. That is, based on what’s the most widely used payment method on your website, you can select the best payment gateway with small fees for this particular transaction type. Lastly, remember that you will also need to pay for a merchant account when calculating how much to spend on the online payment solution. 

Customer support

Imagine your payment system goes down. On Black Friday, when you’re supposed to receive and process dozens of orders and payments. What do you do? That’s right, you contact PG customer service. Once your payment solution is not working, you need to fix this in no time so that your clients can make their purchases. That’s why it’s so essential to have a payment gateway with fast, reliable, and available customer support. 

Merchant account providers

If you want an all-included online payment system, you can select the one that helps with opening a merchant account. Of course, it’s not obligatory, but using all tools from one provider can simplify your daily tasks as a seller significantly.

What are the best online payment systems for e-commerce?

Payment solutions are not something new on the market, but with every year, their number is increasing. It can be quite confusing to choose between well-known names in the industry and brand-new products that exist less than a year. No worries, we’ve prepared a short overview of the most popular online payment systems so that you can compare and contrast what all these companies bring to the table for you and your business. Let’s get started:


Genome is an electronic money institution licensed and supervised by the Bank of Lithuania. Our platform is a great option for both personal users and companies, as we offer seamless, quick, and simple personal, business, and merchant account opening that is done completely online.

Once a company opens a business wallet within Genome, it can apply for a merchant account, as well as benefit from multiple services we provide. Such as SEPA, SWIFT, and internal instant transfers, multiple multi-currency accounts opening that takes minutes, access management feature for shared account access, and a business referral program.

Provide all the necessary documents online and start a merchant account. With it, you can accept payments in over 20 currencies and allow clients to pay with cards, as well as 40 alternative payment methods like Alipay, Paysafecard, Neteller, Skrill, and more!

Our merchants can oversee all the transfers, transactions, and other metrics from one dashboard – anytime and anywhere they like. Genome provides clients with many types of reports for them to track their business performance. Among them are chargeback, approve ratio, transaction reports, etc.

Moreover, we have integrations with many ecommerce platforms and marketplaces. All merchants need is to download our free plugin, and they can use our merchant account in conjunction with platforms like Shopify, WooCommerce, PrestaShop, OpenCart, OXID, and more!

With a Genome merchant account, you can access not only all the needed tools for accepting online payments but also an AI-powered fraud-prevention platform, Covery. It will automatically track and send you reports on suspicious transactions from your customers.


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It’s a well-known and established name all over the world. With almost 300 million active users, this online payment service is one of the most popular and reliable ones both for merchants and their customers. PayPal’s PG is called Payflow Gateway and is easily integrated on any website, but you might still need a developer’s help for this. During checkout, your clients will not stay on-site but will be redirected to the payment platform. 

Among the biggest advantages of this system are a simple setup and great user experience. If you do not have a large pool of loyal customers yet, you may attract new buyers by using PayPal. People are familiar with it and are more likely to trust e-commerce companies that use recognizable payment solutions. PayPal supports different card types (Mastercard, Visa, Discover, and American Express), as well as numerous currencies. Payflow Gateway is suitable for all the following types of payments: credit cards, debit cards, PayPal wallet, Venmo, and PayPal Credit. 

One more pro of this service is its integrations with such e-commerce platforms as WooCommerce, Squarespace, and Shopify. Finally, PayPal’s processing time is very fast compared to other payment gateways. When it comes to disadvantages, PayPal has pretty high fees if your sales volume is low. 


Here comes one more payment system with a well-trusted and familiar name. Unsurprisingly, Amazon Pay has a range of benefits that are connected with the Amazon platform itself. Firstly, the checkout process is incredibly fast for those buyers who are logged into their Amazon accounts. Secondly, it allows customers to complete their transactions on the merchant’s website. Thirdly, Amazon Pay is secure because it can verify customers’ data based on their trusted Amazon profiles. Last but not least, this online payment service is seamless and easily customizable due to the free plugins and manuals. 

While talking about Amazon Pay’s cons, we should mention that it only operates in 18 countries and supports only 12 currencies. One more disadvantage is that this PG does not accept PayPal payments, which can become a problem for some potential clients. The settlement period for this payment gateway is also pretty long – from 2 to 5 business days. Amazon Pay’s customer support is only available via email, which can complicate and prolong the communication process if you need something fixed urgently.  


It’s a full-service e-commerce payment system with a wide range of tools for all kinds of businesses. The main advantage of Stripe is that it offers both payment gateway and merchant account services, which is very convenient, especially for those companies who only start selling their goods. One more benefit is that merchants can customize their checkout page due to the UI toolkit. Even though Stripe offers plenty of manuals and guidelines, the businesses that use its API will make the most out of the service. 

Stripe supports all kinds of payments, including recurring ones. This can be in use for subscription businesses, such as magazines. The lowest fees this PSP has for processing European bank cards, while other transactions will be charged similarly to all the other PGs on the market. 

All in all, Stripe looks like a great tool for managing your online payments. However, its major disadvantage is unfavorable rates for non-EU cards. Consequently, if you’re selling mostly outside of the EU, you can consider some other payment gateways. 


It’s one more service with a full e-commerce package to start selling online right away. Shopify is one of the cheapest payment solutions that comes with a free 14-day trial. That’s how you can explore all the tools and get to know if they fit your needs as a merchant. 

The biggest pro of Shopify is low fees. Despite a pretty limited range of features, this payment system is a great match for small businesses. Another benefit is that Shopify has over more than 100 customizable themes to make your website unique, recognizable, and user-friendly. 

If you choose Shopify to manage your online sales, you need to use its payment gateway along with all the other tools. If you go for PG from some other provider, the fees will increase. This is probably one of the few disadvantages of this online payment solution. 

Other payment systems to consider

Among other popular players on the market are Payoneer, Square, Worldpay, Sage Pay, Cardstream, Pay Cafe, Payment Depot, Visa Checkout, Masterpass, and American Express. You can even go for Apple Pay or Google Pay services. The last ones offer simple and limited functionality, but they are free of charge.

As you can see, there’s plenty of online payment systems for e-commerce to pick out from. Get to know everything you can about your potential clients, their preferred payment options, and then you should be able to select the best payment solution for your online sales.


What payment system is best?

There’s no such thing as the best online payment system as each business is unique. The same goes for your clients. Let’s say, some customers prefer card payments, while others tend to pay with their PayPal accounts. That’s why before selecting an efficient payment solution for your company, you should know your potential clients. Only after this, you can look for the provider that offers all the features you need to manage your online store. 

Without a doubt, such giants as Amazon or PayPal have already built a strong reputation as reliable payment systems that really work. What’s more, they have many different features to choose from that will probably fit any business out there. However, you can also go for some smaller online payment solution if it has all you need. 

How much do payment gateways cost?

All payment systems have different pricing on their PG services. The price will also vary based on the average amount of your transactions, as well as their number. You can check approximate fees in the following table: 

PGPricingBest for
PayPal2.9%+ £0.20 (no monthly fee)Transfers
Amazon Pay2.7% + £0.30 (no monthly fee)Easy to use
Stripe2.9%+ £0.20 (no monthly fee)Full-service payment solution
Shopify Payments2.2% + 20p (with basic Shopify package)Non-EU card payments

What are the different types of e-commerce payment systems?

The E-commerce payment system is a mode of payment without using cash or cheques. With the development of financial technologies, more and more such systems become available to a wide range of people. As of now, the most common e-commerce payment systems are: 

  • Credit and debit card payments (both physical and virtual cards)
  • Bank transfers
  • Digital wallets (PayPal)
  • Mobile banking (usually with the help of Google/Apple Pay)

What is the most popular payment method online?

It depends on the country, industry, and many other factors. Card payments are still very common all over the world when it comes to online payments. Nevertheless, such methods as digital wallets are also on the rise during the past few years.