In the world of online payment options, there has never been more choice. Thankfully, it has also never been simpler to begin accepting payments online. But which system will be right for you? Whether you’re just starting out, looking for a change in system, or have been operating for years without accepting online payments, this article is for you.

How to choose the best online payment system for your small business

Retail. Ecommerce. Payment


We’re going to take you through the things to consider when choosing an online payment system for your business, to help make the process a little easier. We’ll be covering features and fees, as well as including links to some of the most popular systems out there.

What to look for in an online payment system

Intuitive and straightforward

Your payment system should integrate within your checkout process in a way that is intuitive and easy for your customers to use. When it comes to online selling, what seems like the tiniest thing could cost you a sale, so make sure you cover this off before unleashing it on your site. Have your friends and family make trial purchases and see if they struggle with the system in any way.


This is the part where you type the company name followed by ‘reviews’ in Google. Make sure you’re signing up with a payment system that isn’t going to cause you headaches in the future. Another good place to search for discussions on a certain brand or product is Twitter.

Supported by existing software

Is your potential online payment system supported by existing third party software on your site? If it’s not compatible, you may want to move on to the next option, as changing software and other technology on your site is much more difficult.

Available in your country and currency

It seems obvious, but this can be an easy thing to overlook in the initial research phase. Many brands only operate within the USA and Canada, so if you’re not running your business from there you’ll need to choose another online payment system. Ruling this out from the start will save you some time.

Onsite or offsite transactions

This is down to your preference. Some systems will integrate seamlessly within your checkout process, while others will take customers offsite to complete the transaction. For a full user experience we’d recommend a payment system that can keep transactions on your own site from start to finish.

Payment types

Certain systems will have restrictions on some forms of payment. Most will accept MasterCard and Visa credit cards, but you may want to check up on American Express and debit cards. It’s also worth checking if your provider will make users login to an account or if they will have the option to pay with credit card. For example, with PayPal, users can login to their PayPal account or simply pay on credit card without requiring a PayPal account. If your customers are made to sign up for an account they may abandon the sale.

Recurring payment functionality

Is your service or product a membership, subscription, or something requiring an automated recurring payment? This will be important when choosing an online payment system. Ensure that this feature is available before making your decision.

Technical support

Is the system provider going to be available if something goes wrong with their product on your site? Good technical support should be offered and is an important feature to look out for. It’s also worth checking if your preferred method of communication is an option, e.g. phone, email, online chat. While not a deal breaker, support via your preferred method may help guide you to the best decision.

Shopping vs. service

Some online payment systems are geared towards retail and sites with shopping carts, while others are more focused on payments for services, e.g. tradesmen, lawyers, or anyone else being paid for their time. Make sure you’re taking note of this during your research phase.

Security features

It’s important that your online payment system is secure. Security features can get very high tech, depending on how big your site is, but the key ones you should look for are options for CVV2 verification, billing address verification, and VeriSign SSL certificates.

Fees for online payment systems

Of course, cost is one of the main items to look out for when choosing your provider and the right option will vary greatly from business to business. Some things you should know:

Fees per transaction

All providers charge a fee per transaction. This could be charged in the following three forms:

  1. A flat fee
  2. A fee based on a percentage of the transaction value
  3. A flat fee + percentage of transaction value

Some other fees you may come across are monthly fees, one time set up fees, or support fees. These vary depending on your provider, so just make sure you read the fine print.

Volume discount

If you think you’ll be racking up a lot of sales, you should also look out for whether your online payment provider offers a volume discount. This means the percentage fee decreases as your number of sales increases. Keep this in mind when choosing your provider.

Popular online payment systems and their fees

Fees change a lot, so instead of listing them here, we’ve linked directly to eleven of the most popular payment systems around.

  1. PayPal
  2. Google Wallet
  3. net
  4. Skrill
  5. Amazon Payments
  6. 2Checkout
  7. WePay
  8. Dwolla
  9. Paga
  10. Apple Pay
  11. WorldPay

Have we missed out any of your beloved payment system? Feel free to let us know which ones we have missed out.

About Author

Amanda Layton
Amanda Layton
Amanda is a digital marketing professional who blogs for PrognoStore. She is from Sydney, Australia and loves to write from exotic locations.
Add Comment
29 days ago
Love this post. Thanks Amanda. Having read a post on Apple Pay and seeing the possibilities, I think its the benchmark and certainly looks a sure bet for the future. This will in no way eliminate the other players listed here. Imagining making payments at a store's check out with your Apple ID? That's the future with no complications
29 days ago
I will put it down to oversight, but surely Stripe ought to be on that list? Well written article though...I will give you that, so thanks!
29 days ago
I agree with you Susan, Stripe should be on that list. A well written post no doubt
29 days ago
Wow! I'd say this is the definitive checklist to choosing a pos software.
23 days ago
Most of l the payment platforms shown above cannot be used successfully in developing countries without incurring huge transaction costs. The issue of choosing to have the payment page on your site may not be available in developing countries, they just have to make do with what has been provided unfortunately, a payment page outside of their system.
Jusper Korir
23 days ago
Is Amazon Payments the same as Payoneer? I am just curious to know. Thanks for sharing the above payment options. Really helpful.