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How to Pick a Payment System For Your Ecommerce Store

19 min read

When you start an ecommerce business, you should think carefully about how to receive payments online. You need to meet customer needs and manage your business’s cash flow effectively. How your customers pay for your products also determines the tools your business will need (for example, card readers for accepting payments in person.)

Popular payment methods include cash, checks, credit or debit cards, money orders, bank transfers, and online payment gateways such as PayPal.

No matter what kind of business you run, you need a reliable method of accepting online payments. Therefore, you should choose your payment processor and gateway carefully.

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How Online Payment Systems Work

It is often hard to understand how the payment process works, especially the difference between a payment processor and a payment gateway. Let’s figure it out together.

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 the customer, the merchant, the issuing bank, and the acquiring bank. Also, the payment processor typically provides you with a credit card machine and any other equipment you may need to accept credit card payments in person.

A payment gateway securely authorizes payments for online stores. In order to protect your customers’ privacy, businesses cannot transmit transaction information directly from your website to a payment processor. The payment gateway acts as a guard between the customer’s information and the banks.

What to Look for in a Payment Gateway

The payment gateway you choose will impact your customers’ overall experience when making a purchase at your store, and also determines your workflow. Of course, you don’t want a gateway that regularly creates problems for you and your customers. But choosing the right one can be overwhelming. Let’s look at the main factors to make the right decision.

Payment Card Industry Data Security Standard Compliance

The Payment Card Industry Data Security Standard (PCI DSS) is a security protocol issued by the five major payment card companies (American Express, Discover, JCB, MasterCard, and Visa) to protect cardholder data and reduce data breaches. Regardless of your business’s size, if you want to accept card payments, you have to follow the PCI DSS.

Check whether a payment processor complies with the Payment Card Industry Data Security Standard (PCI DSS). Otherwise, you may be at risk for countless bad situations, from data breaches to investigations into your business. Find out what happens if your company’s data gets breached.

Effective fraud prevention

Payment security is a vital factor of a payment gateway. According to a report from Fidelity National Information Services, some 38% of merchants lost at least 6% of their revenue to payment fraud in 2020. If you have a small business, you are more vulnerable to attacks than larger businesses. Whereas big companies likely have an abundance of anti-fraud practices and protections, small businesses may not have any protection and become a target for fraudsters.

Let’s look at a few of the most effective methods to 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 verify with the issuing bank.
  • Card Verification Value (CVV): The CVV (or Card Verification Value Code ) is the 3- or 4-digit code that is on every credit card. This number is only found on physical cards, so the cardholder must have their card in hand to make a purchase online. This prevents credit card and identity fraud because even if someone has a card number and correct address, they will be unable to make a virtual purchase without the CVV.
  • Flag Large Transactions: Fraudsters may take a shot at making large transactions before the stolen card is blocked. Some gateways will flag large transactions and require manual approval from the merchant before proceeding.”>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 an authentication method that secures online transactions for customers. This method allows cardholders to create a PIN to confirm their identity during checkout. By implementing 3D Secure, merchants have chargeback protection and lower interchange rates (fees paid between banks for the acceptance of card-based transactions).
  • Risk Scoring: Risk scores use statistical models that are designed to recognize fraudulent transactions based on a number of rules. During the checkout, the model determines if the transaction is 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. Rules can include failing an address verification test, weird IP addresses, use of anonymous emails, and more.

Make sure that the payment gateway you choose implements 3D Secure and complies with the PCI Data Security Standard in order to best protect yourself and your business.


Money means a lot for any business, so it is better to check twice whether you can afford the payment gateway you want to use. Some may have better features, but they can be more expensive.

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 of service to be sure there are no hidden fees.

Payment method coverage

Letting your customers pay in their preferred way is the best way to gain their trust, and earn more income. Of course, traditional credit and debit cards are still the most common online payment methods, but digital wallets and other alternatives such as Apple Pay and Google Pay are becoming increasingly popular every day.

Also read: Google Pay for Ecommerce Businesses: How It Works

How to Accept Payments With Ecwid by Lightspeed

When it comes to online payments, your customers want flexibility. In order to provide convenient payment options, you need to choose ecommerce software integrated with many different payment systems. Ecwid by Lightspeed is an example of a platform that supports over 100 payment providers.

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

To make this part of the process a little bit simpler for you, we’ve gathered a list of the most popular (and in our opinion, best) payment systems that integrate with Ecwid. We have even outlined some of the advantages, disadvantages, and setup processes for each one, according to how customers like to pay. Easy, right?

Payment Icons-02

Credit cards

Credit cards are by far the most popular payment method. Card payments online are similar to in-store. 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.

When choosing a payment system for credit cards, make sure to check the fees and whether the system is even supported in your country. If you are selling products with restrictions (like guns, drugs, etc.), you may also be limited in your credit card payment processing options because some gateways do not permit these types of transactions.

If you use Ecwid, customers can do everything on the checkout page of your store without being redirected to a separate 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. You can unlock this feature by using Lightspeed Payments, Stripe, WePay, Square, American Express, PayFlow Link, Payments Advanced, and PayPal Payments Pro Hosted.

Lightspeed Payments

Lightspeed Payments is the easiest and most cost-effective way to start getting paid in your online store. Customers can use all major credit and debit cards, as well as Google Pay and Apple Pay. It is available in the United States.

Advantages: Lightspeed Payments has competitive transaction fees (2.9% + $.30 per online transaction) compared to other payment methods and doesn’t have any monthly or setup fees.

You can easily set up and access your Lightspeed Payments right in the Ecwid Control Panel, making it easy to manage your payments. Plus, if you have a question or need help, you can easily contact the Customer Care team via the live chat in the Ecwid Control Panel.

Disadvantages: Currently available in the US only.

How to set it up in Ecwid →


Stripe is a customizable payment method that’s optimized for both desktop and mobile. Stripe payments work in 47 countries.

Advantages: 135+ currencies accepted with the customizable checkout process, which is very easy to set up 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. Stripe also supports recurring subscriptions allowing you to charge customers on a repeated schedule for products and services.

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

How to set it up in Ecwid →

Chase Integrated Payments by WePay

Chase Integrated Payments by WePay is one of the quickest and inexpensive ways to accept credit cards, debit cards, and direct bank payments in your store. It 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.

How to set it up in Ecwid → 


Square is a payment-processing gateway that allows users to make payments directly on your site without having to navigate to an external portal. Square is available in the USA, UK, Ireland, Canada, Australia, and Japan. It also accepts each country’s currency.

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

Disadvantages: Not all countries are included.

How to set it up in Ecwid → 

You can also run offline transactions through Square, creating a synchronized store from using the Square POS inventory. When you’re selling in person, you can process debit and credit cards with your smartphone or tablet using the Ecwid app for Square POS.

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 over the age of 18.

Advantages: Securely accepts 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 → 

Payment Icons-01

Electronic Payment Systems

Electronic Payment Systems are even faster than credit cards. When a buyer chooses to pay with their electronic wallet, they are automatically redirected to the payment site. Then they enter their username and password to confirm the payment. After that, money transfers directly into your Ecwid account.


Ecwid works with a suite of PayPal gateways, such as PayPal Checkout, PayPal Plus, PayPal Payments Advanced, and PayPal Here. That being said, you can approach setting up PayPal in a variety of ways. We’ll break down one of them–check out the pros and cons of PayPal Checkout below.

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

Disadvantages: PayPal has lengthy terms of service, and 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 →

Payment Icons-03

Manual Payment Methods

If you want to accept cash, checks, or wire transfers in your online store, make sure to write clear instructions for your customers.


The simplest and safest way to get paid is cash, if you can meet your customer in person. This 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, if you deliver.

Advantages: A simple way to get money for orders.

Disadvantages: You get the payment only after delivery, or a customer may never pick up their 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 box address, company name, buyer’s full name, and job position at checkout. Purchased orders are then sent to a seller, so that they fulfill them,and deliver the items on the agreed date. The seller will then send a bill or sales invoice for the purchased items.

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 payment you like.

Picking The Right Payment System: The More the Merrier

As you can see, there are many different options to consider, and you should use as many payment options as possible so your clients have a wide variety of options.

For example, it’s good to have PayPal as a payment method because it is highly secure for users. However, some people might not have a PayPal account or want to use their credit card instead. That’s where these other services, like Lightspeed Payments, come in.

When you enable multiple payment options for users, you help them complete the checkout process as quickly and painlessly as possible with the option that best suits their individual needs.

Learn more about picking your payment methods in our Help Center.

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. 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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So simple to use – even my most technophobic clients can manage. Easy to install, quick to set up. Light years ahead of other shop plugins.
I’m so impressed I’ve recommended it to my website clients and am now using it for my own store along with four others for which I webmaster. Beautiful coding, excellent top-notch support, great documentation, fantastic how-to videos. Thank you so much Ecwid, you rock!
I’ve used Ecwid and I love the platform itself. Everything is so simplified it’s insane. I love how you have different options to choose shipping carriers, to be able to put in so many different variants. It’s a pretty open e-commerce gateway.
Easy to use, affordable (and a free option if starting off). Looks professional, many templates to select from. The App is my favorite feature as I can manage my store right from my phone. Highly recommended 👌👍
I like that Ecwid was easy to start and to use. Even for a person like me, without any technical background. Very well written help articles. And the support team is the best for my opinion.
For everything it has to offer, ECWID is incredibly easy to set up. Highly recommend! I did a lot of research and tried about 3 other competitors. Just try ECWID and you'll be online in no time.

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