- 10/28/2013


How to Choose the Right Payment System for Your Business

Whenever you are setting up your online business, one of the most important choices you can make for your bottom line and your customers is which payment system to use for your shopping cart system.

In this post, we’re going to look at the primary features you need to analyze and give you a quick comparison of the top payment solutions available for online businesses.

Important Payment System Features

As you are deciding on the right payment solution for your online business, here are some of the features you need to review to ensure you make the right choice.


While choosing the payment system with the lowest fees shouldn’t be the main goal, it should be one of the first things you consider. You’ll want to know if there are setup fees, monthly fees, transaction fees, cancellation fees, chargeback fees, and so forth.

In particular, be sure to note if the transaction fees are flat or vary based on the number of transactions. If your business doesn’t do a high volume of transactions, it may be best to find a payment system that uses a flat rate fee system as opposed to one that only offers lower fee rates for businesses with a high volume of transactions.

Ease of Use

How easy is the payment system to use for your customers? The last thing you want when you choose a payment system is to choose one that makes it difficult for customers to complete their purchase. If possible, test sites using each payment system to see how quickly customers can complete a transaction, both on their desktops and mobile devices.


Another consideration will be whether you and your users worldwide will be able to use the payment system you choose. While most support businesses and customers worldwide, systems like PayPal specify a list of supported countries. While many countries are able to use their system, there are still some countries who are left out.

Payment Options

For most businesses, customers make a single payment at the time of transaction to complete their order, which is what most payment systems can handle. If your business offers payment plans, deferred payment, or products with recurring fees, you will need to make sure the payment system you choose can handle those types of payment options.

Withdrawal Options

Getting money from your payment system to your bank account should be fast and painless. See what the options are for you to access the money collected by your payment system. If you can transfer it to your bank, how long will the transfer take and are there any associated fees? If you can get a debit card, are there any fees for using it?


If you choose e-commerce platforms like Shopify or Bigcommerce, you will want to find out which payment systems easily integrate with their platforms. If you just sell a few products without a shopping cart, find out which payment system has the best options for buy it now buttons, buttons to show additional purchasing options, and systems that have their own shopping cart.

Comparison of the Top Payment Systems

Now that you know what you should be on the lookout for, here are some of the top payment systems and basic stats about each.

  • Amazon Payments only charges 2.9% + $0.30 per transaction – no monthly fees, setup fees, or other fees will be applied. Businesses with an average transaction volume of $3,000 or more can contact them for a volume discount on the per transaction fee. Amazon customers can easily make a purchase using the information stored in their Amazon account on any website using the Amazon Payments system.

  • PayPal charges 2.9% + $0.30 per transaction (with volume discounts available). Most businesses will be able to use a standard account, which has no monthly fees. Businesses who need additional features such as being able to take credit cards by phone or creating custom checkout pages will have to pay a monthly fee for their advanced or pro account. PayPal has their own card swiper to accept payments in person and a debit card for instant access to funds within a PayPal account.

  • Stripe charges 2.9% + $0.30 per transaction (with volume discounts available). Stripe is a developer-friendly system with thousands of APIs to work with. They also have stylish checkout forms that work great with desktop or mobile users.

  • Authorize.Net charges a lower transaction fee of $0.10 per transaction, but this comes with a $99 setup fee and a $20 monthly gateway fee. They also offer a wider variety of payment portals including online, telephone, mobile, and retail.

  • Braintree charges 2.9% + $0.30 per transaction (with volume discounts available). Payments can be accepted on your website or inside your mobile application.

What is the most important factor for you when choosing a payment system? Please share in the comments.

Updated November 17, 2017.