Ecommerce Payment Processing

Quick reference guide to ecommerce payment processing

13 min read
Marcus Burnette

One of the most complex parts of an ecommerce business is setting up processing services to accept payments online, which is why we’ve created this guide to ecommerce payment processing.

It’s designed to help you navigate the numerous payment methods you can accept, along with some terms that you should know to get up and running with ecommerce payment processing.

We hope this guide serves as a handy quick reference to help you get clients online and selling more quickly, or to assist you in getting the most from your own ecommerce operation.

Types of online payments

Knowing how payment processing works and what kind of payments you can accept is the first thing you’ll need to consider before signing up for a payment processor.

Credit cards

Almost all payment processors will allow you to accept credit card payments from your customers, which is one of the most common ways to pay online.

Credit card payments typically go through the following lifecycle:

  1. Customer enters payment details on your site
  2. These details are securely sent from your site to your payment gateway to check if the transaction should be approved or declined
  3. Your payment gateway makes the determination on the transaction, and tells your site if it’s good or not
  4. Your site either accepts the payment and completes checkout, or shows the customer a decline message and rejects the payment

The Wi-Fi symbol in the credit indicates that they can be used for contactless payments with the help of a contactless-enabled point of sale or tap to pay on phone.

GoDaddy Payments

If you’re one of the many people building an ecommerce store using WordPress and WooCommerce, we recommend GoDaddy Payments. It’s a proven, easy and profitable POS system optimized for WooCommerce, with these key features and benefits:

  • Manage everything in one place — Online and in person transactions all handled in one location, under one WooCommerce dashboard.
  • Keep more of what you sell — Rely on the lowest debit and credit card processing fees, starting at 2.3%, plus $0.30 per transaction. There are no long-term contracts, set up fees or hidden charges.
  • Save time and start selling faster — Avoid tricky payments integrations and start selling faster with an integrated POS system designed for quick setup and built to work with WooCommerce.
  • Accept payments anywhere, anytime — Provide convenient in-person credit and debit card payments options that let your customers pay the way they want: swipe, insert or tap.
  • Rely on a proven, reliable POS solution — Gain peace of mind with a reliable and versatile POS system able to meet any in-person selling need with billions of dollars in transactions already processed


PayPal is one of the most trusted payment methods on the internet, and it’s a huge benefit for merchants to offer it. Nielsen Online Buyer Insights reports that PayPal Merchants benefit from a 27% increase in total customers after integrating PayPal, while total amount spent by customers increases 15% and transactions per customer almost double.

PayPal can process credit card transactions, but they can also act as a money transfer service when PayPal credit is used (like a digital wallet).

This is especially useful when selling internationally, where some customers may not have an accepted credit card type.

ACH transfers / eChecks

Bank transfers or eChecks are essentially like paying with cash or checks online. They allow the customer to enter bank details for your payment gateway to check the funds and initiate a transfer to your merchant account.

There are also some payment methods, such as Dwolla, that can simulate “cash transfers” online, which are typically lower cost for merchants than credit card processing.

Bitcoin / Cryptocurrency

Bitcoin is still a very small portion of online payments, so many merchants don’t yet accept bitcoin or other cryptocurrencies. However, if your customers are concerned with privacy, bitcoin may be an option they appreciate having (though otherwise you probably shouldn’t bother with it for your store).

Bitcoin transfers are sort of like a secure ACH transfer (but in a unique currency rather than USD, etc), as the transfer is immediate and there are no payment processing fees.

However, the complex setup really isn’t a great option for beginners, so while it can seem like a cutting edge thing to do, you’re better off with PayPal and/or credit card payments.

Payment processing terms

Let’s take a look at a glossary of ecommerce payment processing terms with which you’ll want to be familiar as you launch your business. These are mostly related to credit card processing, as that’s typically a rabbit hole for many new merchants.

Merchant account

A merchant account is essentially your bank account for transferred payments; it’s where the payment coming from the customer goes first before you can transfer it out to your business bank account (if you have a separate business bank account).

The merchant account isn’t involved directly in the payment transaction, so you have a lot of flexibility in where you get your merchant account (i.e., your local bank).

If you have a brick-and-mortar location, you most likely already have a merchant account for the payments you accept in-person. If you don’t already have one, you have a choice between a dedicated or an aggregated account.

A dedicated account will be a merchant account only used by you, and is the choice of many merchants (though you’ll typically need some more set up to get a dedicated account). When payments are processed, they’re typically transferred to this account within a couple of days, and then released to you for transfer to your business bank account within a couple more days.

An aggregated account is what many modern processors like GoDaddy Payments, Braintree, and Stripe offer — they’re bundled in with your payment gateway so you don’t have to sign up for both a merchant account and a payment gateway account. They’re especially great for new merchants, as you only sign up for one “payment processing” account, and after payments have cleared, they can just be transferred right to your business’s bank account.

Payment gateway

A payment gateway is the online replacement for a point-of-sale terminal (the thing your credit card is swiped through). This is what handles approving and declining transactions and managing responses to and from your website.

When you use an ecommerce plugin, you typically need an extension or add-on plugin to connect your payment gateway to your website.

The integration plugin is what handles the communication between your website and the payment gateway to check whether transactions should be approved or declined.

You can usually buy a premade integration for your ecommerce plugin and your payment gateway. If none are available, you may need to hire a developer to build one, as your website needs a way to communicate with your payment gateway.

If you have a dedicated merchant account, you may be charged fees for it, and your payment gateway fees will be assessed separately. If you sign up for an aggregated account that includes both the merchant account and payment gateway, your fees are typically for the entire “payment processing” package.

The payment gateway is where you get differentiation in terms of which features are offered: whether customers can save cards for future purchases, whether you can authorize charges and capture them at a later date, and which credit cards (or other payment methods, such as eChecks) you can accept.

Charge vs. authorize

Most payment gateways can allow you to either charge or authorize a payment. Charging a payment means that your payment gateway requests funds from the customer immediately; a charge says, “please have this person’s account pay me now.”

Authorizing a payment means that your payment gateway first asks if the customer can pay the charge; it says, “does the customer have sufficient funds for the order?” This lets you then capture the payment and complete the charge later.


Tokenization refers to the ability to securely save a customer’s payment information for a later date. You should never, ever, ever store customers’ credit card numbers on your website. Instead, if you want to allow customers to save a payment method for easy use in the future or for recurring payments, your payment gateway will need to offer the ability to tokenize the payment details.

This means that the payment gateway securely stores the customer’s credit card number and personal details, and instead gives your site a “token” to use.

This is kind of like how poker chips work — the payment processor gives you a token for the credit card number instead of the actual credit card number. At a later time, you can charge the customer by using the payment token — your website basically says to the payment gateway, “Please charge token #123456,” and the payment gateway can then run the credit card details for that token securely since it has stored which tokens go with which credit card.

That way, if your site is ever compromised, only useless payment tokens are gathered (since they’re specific to your merchant account, they can’t be used by anyone else), rather than very important credit card numbers.

If you’d like to allow customers to save payment methods for future use, or you want to allow things like pre-orders and recurring payments, you’ll want to ensure that your payment processor supports tokenization. They sometimes also refer to this as a “secure vault” or similar.

SSL certificate

Here’s what you need to know about SSL certificates: get one. That’s it.

Truly though, get one no matter whether your payment processor requires one or not; it’s a no-brainer investment and you can get them starting for less than $10 per year.

Not only do SSL certificates protect customer information when your payment processing takes place on-site, they also protect login credentials — both yours and customers’ — when logging into your site, so they can’t be intercepted.

Additionally, they also improve conversions. Customers are trained to look for the “green lock” at checkout, and even if they’re being taken off-site to complete a purchase, they still expect to see it on your cart and checkout pages. Just get one.

If you don’t already have an SSL certificate for your site, there are a number of great places that you can purchase one to secure your site. In addition, most modern hosting providers also include an SSL certificate with their hosting packages, so make sure to check with your hosting provider first to see if this is an included feature you’re not yet utilizing.

PCI compliance

PCI Compliance is one of those terms that many merchants have heard of and know is important, but don’t really understand what’s related to it or how it works.

PCI Compliance refers to regulations that are imposed on merchants in order to be able to accept payments securely online.

There are several levels of compliance, which relate to different layers of security for payment processing, and merchant accounts can require different levels of compliance to accept payments (or some allow the use of an SSL certificate alone and charge a monthly fee for non-compliance).

Since payment processing requires communication between your site and a payment processor, it may or may not be related to your payment gateway / ecommerce plugin alone, which is why it tends to be complicated to understand.

If payments occur outside of your site, and the customer gets redirected back to your site (like PayPal Standard), this is PCI compliant because your site never handles sensitive customer data or credit card numbers.

If customers remain on-site, then the way your payment gateway integration is built and the features your payment gateway offers will influence PCI compliance.

Find out more about PCI Compliance.

Helpful resources on payment processing

This guide gives you an introduction to the types of processing and some of the terms payment processors use, but deciding which processor is the best one for your store is up to you. It will depend largely on:

  • What payments you need to accept (credit cards, ACH / eChecks, etc)
  • Whether you have a merchant account already or not
  • Whether you need to be PCI compliant and what level of compliance you need to meet
  • Whether or not there’s an integration plugin available for your ecommerce plugin and payment gateway (you’ll have to fund one if not)
  • What features the payment gateway offers
  • What features the payment gateway integration plugin supports (if it can tokenize cards using your payment gateway’s tokenization, etc)

If you use an ecommerce plugin already, we’ve also compared some of the payment gateway integration plugins available for each:

Payment processing recommendations

So which payment processors do we recommend? That depends on how you currently have things set up.

One of the easiest ways to get set up to accept payments is with our very own GoDaddy Payments. Whether you’re already using one of our managed platforms — like Managed WooCommerce Stores, which has GoDaddy Payments integration built-in — or simply hosting your WooCommerce store elsewhere, integrating GoDaddy Payments is a breeze.

Signup takes just a few minutes to complete and you can begin accepting payments almost immediately — and get funds in your bank account the next day! If you’re hosting your WooCommerce site elsewhere, you simply need to install the Poynt — a GoDaddy Brand for WooCommerce plugin to connect.

As a bonus, GoDaddy Payments also lets you accept payments without a website using Pay Links and a Virtual Terminal, but that’s a whole different article.

If you already have a merchant account (i.e., for your brick-and-mortar store), and you want to use your chosen solution for your online payments as well, you could also check out Braintree. While they offer accounts with combined merchant accounts and payment gateways for new merchants, you can also use their payment processing services with an existing merchant account. They have fantastic customer service, and they offer tons of great tools and features for merchants.

The built-in integration they have for PayPal is also excellent (PayPal owns Braintree). The WooCommerce integration for Braintree supports many of these features.

Many merchants also use Authorize.Net, which is another excellent choice (they were the first company to offer online payment gateway services). They offer tokenization, eCheck support, and tons of other features. You can use Authorize.Net as a payment gateway with an existing merchant account, or use their bundled offering for an all-in-one processor.

Stripe is also quite popular, since it’s really easy to get set up. They offer combined merchant accounts and payment gateway services, so you’ll be up and running within minutes, and almost every ecommerce platform integrates with Stripe.

Closing thoughts on ecommerce payment processing

We certainly recommend taking all the time needed to prioritize the features you need in your payment-processing solution. Needs vary, but we find most online sellers look for something that lets them keep more of their sales, as well as a platform that’s easy to set up yet offers robust functionality.

Whatever you land on, we congratulate you on your wise investment of time in considering our guide to ecommerce payment processing.

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