How to Pick a Payment System For Your E-commerce Store

How to Pick a Payment System For Your E-Сommerce Store

17 min read

When you start an e-commerce business, you should think carefully about how to accept payments online to meet customer needs and manage the cash flow of your business effectively. The payment methods will also determine the facilities your business will need.

Typical payment methods used in a modern business context include cash, checks, credit or debit cards, money orders, bank transfers, and online payment gateways such as PayPal.

Unless you’re running a shady side business that only accepts suitcases full of cash, you’ll need a reliable method of accepting online payments on your website. It means you should choose a payment processor and payment gateway.

How Online Payment Systems Work

It is often hard to understand how the payment process works and what the difference is between a payment processor and a payment gateway. Let’s try to find out.

There are four parties involved with every credit card transaction:

  • The customer
  • The merchant
  • The acquiring bank
  • The issuing bank.

The aim of every transaction is to transmit money from the issuing bank to the acquiring bank according to the agreement between the customer and the merchant. The payment processor and payment gateway help to connect all four parts of the payment chain.

The payment processor executes the transaction by transmitting data between you, the merchant, the issuing bank, and the acquiring bank. It also typically furnishes you with the credit card machines and other equipment you use to accept credit card payments.

A payment gateway securely authorizes payments for online stores. This is necessary because it is prohibited, due to security reasons, to transmit transaction information directly from your website to a payment processor. This gateway is kind of like a guard, or a middle man, between the customer’s information and the banks.

What to Look for in a Payment Gateway

The payment gateway you choose will not only impact the overall customer experience but also determine your casual workflow. Of course, you don’t want a gateway that regularly creates problems for you and your customers. The choice is hard but let’s look at the main factors to make a right decision.

PCI DSS compliance

The Payment Card Industry Data Security Standard (PCI DSS) is a security standard issued by the five largest credit card companies (American Express, Discover, JCB, MasterCard, and Visa) to protect cardholder data and help reduce data breaches. Regardless of your size, if you want to accept card payments, you have to be on good terms with the standard.

Check whether a payment processor complies with the Payment Card Industry Data Security Standard (PCI DSS), otherwise, you may be at risk for data breaches, fines, card replacement costs, costly forensic audits, and investigations into your business, brand damage, and more if a breach occurs.

Effective fraud prevention

Payment security is the vital factor for Payment Gateway. According to The Nilson Report, merchant losses to fraud have been increasing in recent years and it will be even worse in the near future. Moreover, if you have a small business, you are even more vulnerable. Whereas larger companies are more likely to have anti-fraud practices, fraudsters aim at the small business that may not have any protection.

Let’s look at a few of the most effective methods to check transactions and prevent fraud:

  • Address Verification Service (AVS): When customers purchase items, they need to provide their billing address and ZIP code. An AVS will check if this address matches with what the card-issuing bank has on file. As part of a card-not-present (CNP) transaction, the payment gateway can send a request for user verification to the issuing bank.
  • Card Verification Value (CVV): The CVV (or Card Verification Code ) is the 3- or 4-digit code that is on every credit card. It helps to ensure that only the actual physical holder of the card can use it remotely and that someone who has only got the card number and some personal information cannot provide this value without the actual card.
  • Flag Large Transactions: Fraudsters will take a shot at making large transactions before the stolen card is blocked. Such transactions may require the manual approval from the merchant before proceeding.
  • Payer Authentication (3D Secure): 3D Secure adds another authentication step for online payments. Payer authentication, also called Verified by Visa and MasterCard SecureCode, is a cardholder authentication measure that secures online transactions for customers. This method allows cardholders to create a PIN (secure code) that can be used during checkout to confirm the user’s identity. By implementing this, merchants are provided chargeback protection and lower interchange rates.
  • Risk Scoring: The tool uses statistical models designed to recognize fraudulent transactions based on a number of rules. During the checkout, the model determines if the transaction fraudulent. A higher probability of a transaction being fraudulent indicates that you should verify the order. Risk-scoring tools provide a case-by-case evaluation and will flag transactions based on the rules you choose such as AVS failure test, IP range, use of anonymous emails, billing address, and others.

Make sure that the payment gateway is at least integrated with 3D Secure and complies with the PCI Data Security Standard (PCI DSS) we mentioned before.


Money means a lot for any business, so it is better to check twice whether you can afford the payment gateway you are about to choose. Some may have better features, but they will also come with a greater cost.

At first, find out whether a payment processor charges a monthly fee or a flat per-transaction fee. Your choice depends on your business activity, but in any case, go through the full terms to be sure there are no hidden fees.

Payment method coverage

Accepting any form of payment your customer may use is the best way to gain more money. Of course, traditional credit and debit cards are still the most common online payment method, but digital wallets and other alternatives such as Apple Pay and Samsung Pay are becoming increasingly popular every single day.

How to Accept Payments With Ecwid E-Commerce

When it comes to online payments, your customers want flexibility. In order to be able to provide them with convenient payment options, you need to choose e-commerce software that is integrated with many different payment systems. Ecwid E-Commerce is an example of such software, supporting over 50 payment providers to process your transactions.

With so many different options, you could spend hours pouring over the details of different providers.

We wanted to make this part of the process a little bit simpler for you, so we’ve gathered a few of the most popular payment systems that integrate with Ecwid, outlined some of the advantages and disadvantages, and even outlined the setup process for each one. Easy, right? Right.

If you’re looking for a payment system that’s not outlined here, please be sure to check out our full list of online payment systems that you can use in Ecwid.

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Credit cards

Credit cards are by far the most popular payment method. Card payments online are similar to using a payment card in stores. Here’s what happens:

  1. The buyer chooses the payment card. The store redirects the customer to the payment gateway.
  2. The buyer puts in the card number, card name, and CVV (the special security code on the back of the card).
  3. The buyer clicks “Pay,” and the money is debited from the card, after which the buyer automatically returns to the store page and the payment system informs the store: “Okay, the payment was accepted.” Money goes to your account on the same day.

Before you choose an option(s) for credit card processing, it’s important to know that different processing companies have different fees and rates, typically on a per-transaction basis.

Be sure to know the fees before selecting an option, as well as from which countries you can accept payments. If you are selling products with restrictions (like guns, drugs, etc.), you may also be limited in your credit card payment processing options, as some companies do not permit these types of transactions.

With Ecwid E-Commerce, it is possible to pass through the checkout on the checkout page of your store — without redirecting customers to the payment gateway. Technically, the charges are still processed on the payment processor side, but the customer stays in your store when entering the payment information. It’s available with Stripe, WePay, Square, American Express, PayFlow Link, Payments Advanced, and PayPal Payments Pro Hosted.


Stripe is a customizable payment method that’s optimized for both desktop and mobile. Stripe payments work in 39 countries, including the USA and Canada.

Advantages: 135+ currencies accepted with customizable checkout process, very easy setup with Ecwid. No monthly or setup fees. You can also set up Apple Pay with Stripe to offer your customers simpler and faster payments with one-tap checkout.

Disadvantages: Not all countries are included. Check the availability for your country in the list.

How to set it up in Ecwid →


WePay is the quickest and least expensive way to accept credit cards, debit cards, and direct bank payments in your store. With We your customers can proceed to payment on the checkout page, without going to the payment gateway page. It makes your checkout process really fast and comfortable for customers.

At the moment, WePay is available for merchants from the US, Canada, and the UK.

Advantages: fast and easy way to accept payments within your website. Payments and orders are automatically synced, so you can keep track of your business all in one place.

Disadvantages: limited to the United States, the UK, and Canada.

Cost: starts from 2.1 % + 0.2 GBP per transaction. Check your rate here.

How to set it up in Ecwid → 


Square is a payment-processing gateway that allows users to make a payment directly on your site without having to navigate to an external portal. Square is currently available for the USA, Canada, Australia, the UK, and Japan in US, Canadian, and Australian dollars, British pounds, and Japanese yen.

Advantages: fast, easy checkout process directly on your site.

Disadvantages: limited to United States, Canada, Japan, and Australia.

Cost: the fee for all payments processed via Square is 2.9 % + $0.30.

How to set it up in Ecwid → 

If you want to accept physical debit and credit cards on your smartphone or tablet, just use an Ecwid app for Square POS. You can run your online and offline transactions through Square and create a synchronized online store from the Square POS inventory. Check the detailed instructions on how to connect Square POS to Ecwid.

American Express

Thanks to our Amex Ecwid integration, you can set up an American Express payment gateway without having to write a single line of code into your site. This option is open to legal residents of the United States and its territories ages 18+ who are eligible cardholders.

Advantages: Securely accept credit cards directly on your site without having to redirect to a new portal at checkout.

Disadvantages: Only works for American Express card members with businesses within the United States.

How to set it up in Ecwid → 


Bancomer is Mexico’s largest financial institution allowing users to accept payments in Mexican Pesos, Euros, and U.S. Dollars. This online payment method is an idea for Spanish-speaking business operators and shoppers who are located in Mexico.

Advantages: Targeted to Spanish-speaking demographic and built-in capability to process Mexican Pesos as a form of payment.

Disadvantages: If your store’s currency isn’t the same as your Bancomer account’s currency, your payment gateway won’t work.

How to set it up in Ecwid → 

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Electronic Payment Systems

Electronic Payment Systems are even faster than credit cards. The buyer chooses a payment via electronic purse, is automatically redirected to the payment site, enters username and password, and confirms the payment. Then you get money into your account.


Ecwid works with a suite of PayPal solutions such as Standard, Express Checkout, Advanced, Payflow Link, and Payments Pro. That being said, there is a variety of ways you can approach setup. We’ll look at PayPal Standard as an example.

Advantages: Seamlessly integrates with online sites for fast, easy payment, and 100% secure checkout. Allows users to make purchases in a variety of currencies. One of the most versatile payment processing options.

Disadvantages: PayPal has lengthy terms of service, and it has the ability to freeze your account at almost any time. There is also a blurred line on what PayPal deems “obscene” material, which can restrict the sale of certain products they consider inappropriate.

How to set it up in Ecwid →

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Manual Payment Methods

If you want to accept cash, checks, or wire transfers, just write the instructions for your customers.


The simplest way to charge your customers is obviously getting the money cash. It is possible if you offer delivery or in-store pickup. When this payment method is used, a customer is not asked for any payment details at checkout aside from the standard address form.

Advantages: a simple way to get money for the orders.

Disadvantages: you’ll get the payment only after delivery and the customer may just not appear for the order.

How to set it up in Ecwid →

Purchased orders and checks

Purchased orders allow your customers to buy your items using a document issued by a buyer to a seller that notates the types, quantities, and agreed prices for products or services. Essentially, it’s a kind of contract between you and your buyer. When using these, the customer is asked for a PO number, Company name, Buyer’s full name and Job position at checkout. They are then electronically transmitted over the Internet.

Offline check payments require the check Owner’s full name, checking account number and bank routing number. You can use them for any kind of check payments you like.

Picking The Right Payment System: The More the Merrier

As you can see, there are many, many different options to consider–but the bottom line is that you should use as many payment options as possible so your clients have a wide variety of options.

For instance, it’s good to have PayPal as a payment method, but some people might not have a PayPal account. They want to pay via credit card instead. When you enable multiple payment options for users, you help them complete the checkout process as quickly and painlessly as possible–and via the option that best suits their unique needs.

Still Looking for an Online Payment Option?

If you didn’t find what you were looking for in this list, be sure to explore the countless other integrations we have to offer. The right payment processing resource will depend on your location, demographic, and unique business needs, so be sure to take the time to fully explore your options.

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About the author

Ann is Financial Analyst at Ecwid. She moved to finance but still keeps marketing in the heart. Started practicing CrossFit because of the Doberman in the gym.

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