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What Payment Processor Should You Use with Your E-Commerce Site?

What Payment Processor Should You Use with Your E-Commerce Site? post thumbnail image

Payment is an integral part of an e-commerce site. After all, you don’t want to give your products away for free. You want to make money! So every e-commerce site needs to consider what payment system works best for them. Some CMS make the choices easy, like Weebly, while others give you more options. 

So how do you know what payment processor is best for you? We’ll walk you through the basics and give you the information you need to help you make the best choice. 

What is a Payment Processor?

But first, we want to make sure we’re all on the same page concerning what payment processors are. 

A payment processor takes payments from visitors. It’s similar to the physical card reader you use at the store, but virtual! The payment processor completes the payment and sends the necessary information to both the customer’s card and bank, as well as you and your bank (so you can get paid!).  

Many payment processors also store and collect payment information so that you don’t have to, which helps you stay compliant with privacy laws. 

How to Choose the Best Payment Processor for Your Site

Choosing the best payment processor depends on different variables. This means that while a certain payment processor may work well for one site, it may not work well for another. 

So it’s important to take these variables and assess what your business needs before making a decision. 

Consider Your Customers

The first variable to look at is your customers. What payment forms are they likely to want and which ones will they have access to? This is an important assessment since customers may disengage from the checkout process if they get confused or are required to go through additional hoops just to check out. It’s best to use a payment processor that the majority of your customers will be familiar or comfortable with. 

Consider Your Platform

Some e-commerce solutions already have integrated payment processors, like Weebly. This means that you can skip the complicated backend setup and instead use the platform’s easy integration. If this quick and easy integration appeals to you, check your e-commerce platform to see if there are any preconfigured integrations. 

Make Sure it’s PCI Compliant

PCI compliance is a set of standards that make sure the payment processor is secure and trustworthy. So it’s imperative that the one you choose is PCI compliant. Many of the big-name payment processors are PCI compliant, but it never hurts to double check. The last thing you want is to be on the hook because your payment processor wasn’t secure. 

Check the Fees

Payment processor software often comes with fees. After all, they are a business that needs to make money, too. However, not all payment processor fees are created equal. Some fee structures are easier on small businesses, while others make more sense for larger endeavors. 

It’s not always straightforward to find the fee structure, but you should definitely check into whether your chosen payment processor has the following types of fees (and, if they do, how expensive they are):

  • Setup and/or cancellation fees
  • Monthly or Annual Fees
  • Per transaction fees
  • Chargeback fees

Ease of Use

This goes hand-in-hand with our previous tip about considering your customers. You should assess how easy the payment process will be for your customers. By making your checkout process easy, you maximize the chance of someone successfully completing a purchase. If the checkout process isn’t so straightforward, you run the risk of people abandoning their cart without completing. So investing in a payment processor with an easy checkout interface is worth the research. 

Keep Your Currencies in Mind

Accept multiple types of currencies? Then you need to make sure that your payment processor works with all of them. Not all payment processors accept all currencies, so it’s important to find out what currencies they cover before making your decision. 

Valuable Features

Is there a feature you can’t live without? Make sure your potential payment processor has it! For example, you may have an e-commerce site that focuses on recurring payments or subscriptions. You need to make sure that your payment processor is set up to handle payments like that. 

If fraud detection and treatment is important to you, you may want the extra control that comes with a payment processor that has customizable anti-fraud settings.

Overall, what features you want will depend on you, your store, and your customers. If you make a list of desired features and consider the previous points, you may be able to find your perfect payment processor from amongst the options. 

Payment Processors

There are a number of payment processors out there to choose from. If you’re not sure about your options, we’ve put together a list of popular ones to get you started. Each payment processor in the list has a snapshot table that gives each processor’s highlights. 

However, our overviews only catch a fraction of each payment processor. So once you’ve narrowed down a few that interest you, we recommend doing more in-depth research to compare them.  


PayPal is a well-known payment platform. Founded in 1998, PayPal has grown into one of the big payment processors of today. One of it’s main draws is the ability to use for personal or for business. It accepts popular payment methods in 120 countries and even supports in-person card transactions if you have the PayPal card reader. 

PayPal Snapshot
Online + In-Person Payment ProcessorAdvanced Setups can be more expensive than some alternatives 
No need to integrate a checkout system – customer go to PayPal to complete a transactionPayPal requires customers to have a PayPal account to checkout
Supports recurring payments with PayPal Subscriptions


Stripe was founded in 2010 and supports the transactions of millions of companies around the world. With 135+ different currencies and payment methods supported, it processes billions of dollars each year. 

Stripe Snapshot
Developer friendlyCan’t process PayPal payments
No extra charge to use Stripe APIOnline only – no in-person
No monthly feeSupports recurring payments with Stripe Billing


Square entered the payment processing scene in 2009, bringing with it it’s iconic little white card reader. Now it’s a thriving payment processor with both in-person and online solutions.They are a great option for those who want to balance both in-person and online transactions. 

Square is pay per transaction, which works particularly well for small businesses just getting started. If they only have a few sales, they only pay for the sales they have made. 

However, established companies with a greater number of transactions may find that Square can get expensive very quickly with this payment model. While Square works great for new companies, bigger companies might find it more cost efficient to find a payment processor with a monthly payment. 

Square Snapshot
Online + In-Person payment processorNot great for companies with a lot of monthly transactions
Great for businesses with a small number of monthly transactionsTechnical knowledge needed to integrate their checkout system into your e-commerce site
No monthly feesSupports recurring payments with Square Invoices

Amazon Pay

Many are familiar with Amazon shopping, but did you know they also have a payment processor? Amazon Pay allows users to pay on your e-commerce site using their Amazon account. They work with a variety of e-commerce platforms, such as WooCommerce, Drupal Commerce, and Shopify!

Amazon PaySnapshot
Voice ShoppingOnline only – no in-person
Customers can use Amazon account to checkoutNeed an Amazon account to continue checkout
Trusted since many use Amazon shoppingCan’t process PayPal transactions
No extra charge to use the Amazon Pay APISupports recurring payments, but has limits

Founded in 1996, is a subsidiary of VISA. They work with over 430,000 merchants and handle over a billion transactions yearly. On top of that, they won awards for their API integration two years in a row. They also offer advanced fraud detection settings to help you keep your e-commerce site protected. 

Authorize.Net Snapshot
Can accept PayPal transactionsHas monthly and setup Fees
Dedicated fraud detection suite and fraud support teamOnline + In-Person payment processor
Supports automated recurring payments

Choosing a Payment Processor

At the end of the day, you get to decide what payment processor is best for your business. What works for one business may not work for you, so be sure to consider your business’s needs and situation. 

If you’re just in the planning phases and still shopping around for an e-commerce solution, check out our ShopSite, Weebly, and WordPress packages. Each provides a strong base on which to build an e-commerce site. They also come with easy payment processing integrations, many of which are mentioned here. 

You can check out our guides to building an e-commerce site here: 

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