Shopify payment methods for small businesses explained

Setting up a Shopify online store is quick and simple. The platform removes barriers to online selling and makes it easy for small businesses to compete with the big boys.
Perhaps the biggest decision you will make when setting up your online store is the payment methods available. When the whole point of your store is to make money, you need to know how you’re going to get paid. Shopify is known for its large selection of payment methods. You could even get paid in Bitcoin if that works for your business!
In this guide, we will outline how Shopify payments work, which options are available to you and how to choose the right one for your business.

How do Shopify payments work?

When setting up your online store, you need to decide how you are going to get paid. The type of store you are running will have a huge impact on the payment methods you choose.
Shopify offers its own payment portal which allows you to accept credit card payments and other popular payment methods. The payment portal is PCI compliant and supports 3D secure checkouts, to help keep your online store safe. You will pay a monthly subscription for your payment portal. You will also pay a small flat fee and a small percentage of each sale, depending on your plan.
Your sales are deposited into your Shopify account and then paid to your chosen account in scheduled payouts. Remember that every third-party payment provider will take a cut. The Shopify Payments portal offers ease and simplicity that is easily integrated with your store, so it is often worth parting with a percentage to make it easier to secure sales.

Understanding the Payment Providers

In addition to the Shopify Payments portal, you can also upgrade your online store with a variety of secure payment apps.

Credit and debit card payments

The vast majority of internet users want to pay by credit card. Offering credit card payments will inspire trust in visitors and make them feel more confident about shopping with you. Credit cards also offer a degree of protection for the customer and the retailer. Fraud prevention checks will allow you to feel confident that customers aren’t shopping with stolen card details.
All credit card payments are managed through Shopify Payments. You don’t have to set up an account with any third-party payment provider and your customers will enjoy a seamless experience.

Quick pay options

Another popular option is to use well-known third-party sites to enable quick shopping options. These include PayPal, Amazon Pay and Apple Pay. Customers will already have their card and shipping details saved to these sites, so the checkout process is much quicker. These payment options are also available through Shopify Payments.

Instalment options

If you sell high-value items, you may want to allow your customers to split their payments. You will be paid upfront for the entire purchase, but the customer will pay in instalments. If a customer misses a payment, it is down to the third-party to chase the payment. The most well-known split-payment service is Klarna, but others are available.
Some payment instalment apps allow you to split payments between multiple cards, which can be ideal if you sell items that are regularly purchased as gifts.

Deposit and invoice

Another common payment method for large companies is the deposit and invoice payment methods. You might take a deposit for a large value item and then the full amount will be due when the item ships. You can use an app like Deposits & Split Payments‑Depo to manage this type of payment.


If customers can purchase a periodic subscription to your service, a subscription model might be more appropriate. You can choose if your products are only available on subscription, or if you would like to allow one-off payments.

Point of sale integration

If you also run a brick and mortar store and want to unify your stock management, you can choose a point of sale app that will allow your online and offline sales to share a store management system. This will also allow you to cross-promote your online and offline offerings to boost interaction and sales.


Selling items before you even have the stock can be daunting, but it can help to pre-qualify a product and let you know that the demand is there. And if a product sells out, you can continue selling and allow individuals to pre-order for when additional stock lands.

The best Payment Providers for small businesses

The best payment option for your business is the one that will encourage customers to purchase. Offering as many options as possible while still ensuring clarity through the customer journey is one surefire way to success.
The best payment options for your online store will depend on the type of products you sell, your customer’s expectations and your budget. There’s little sense in paying for multiple payment options if the majority of your customers only use a debit or credit card.
Look to your store support inbox to determine which options would be welcomed by your customers. If you open your store only using Shopify Payments but customers are repeatedly asking about other payment options, you know the demand is there.
If you need help setting up your online store, the Auburn team is here to help. Get in touch to find out how we can work together to generate more traffic and more sales for your business.