Shopify accounting: How to manage multiple payment methods

It’s pretty much expected that Shopify stores offer multiple payment methods (otherwise known as payment processors or payment gateways), everything from Shopify Payments, AfterPay, PayPal and more. With a bit of groundwork, you can automate the majority of your Shopify accounting and bookkeeping, even with multiple payment methods.

In this article, we’ll go through why you should consider offering multiple payment methods if you don’t already, as well as the options available to Shopify store owners. Then, we’ll give you an easy to follow guide to automating your accounting and bookkeeping. Finally, we show those with multiple sales channels how to implement the same automation solutions.

Benefits of offering multiple payment methods

The first major benefit of offering multiple payment methods is for your customer’s convenience. Though it may not seem like a major deal, a recent cart abandonment survey actually found that 8% of customers would leave if their preferred payment method wasn’t available. This is even more important if you’re reaching customers in different countries with unique preferences.

Next, offering a variety of payment options creates more security for both your customers and for your store. An online consumer survey found that 40% of people would trust the security of a store that had multiple payment methods compared to a store that only had one. On top of the perceived sense of security, your store is more safe in the scenario where one option crashes.

What payment methods are available for Shopify?

The main payment method available for Shopify store owners is Shopify Payments. You can double check whether Shopify Payments is available in your location. Shopify partnered with Stripe, originally a third-party payment processor, and rebranded it before integrating it into stores. There are credit card processing fees involved for Shopify Payments.

Despite having their own method, Shopify still allows users to integrate other third-party payment solutions such as PayPal and You generally need to pay both credit card processing fees and transaction fees for these third-party options. Additionally, you can link buy-now-pay-later payment methods such as AfterPay and Klarna.

There are dozens, if not hundreds, of payment methods available for Shopify stores. What you select will ultimately depend on who your target market is and what makes sense for your business model. It’s worthwhile to spend time doing market research to figure out what payment methods would be ideal for your customers.

What do I need to automate my Shopify accounting?

Once you’ve selected and set up the payment methods that are relevant to your customers, you can start automating the manual data entry process that’s part of your bookkeeping and accounting. Having an adequate cloud-based accounting software will be the key to automating not only your accounting but other processes as well such as inventory management.

Next, you’ll need an accounting integration. If you’re using Xero, MYOB or QuickBooks Online, you can use Amaka’s Shopify + Xero accounting integration, Shopify + MYOB accounting integration or Shopify + QuickBooks accounting integration. Our solutions automate manual data entry and speed up bank reconciliation, saving you dozens of hours every month.

The accounting integration will automatically sync transactions into a summarised invoice on a daily basis. This includes those from Shopify Payments, Shopify POS, COD, gift cards, refunds and any third-party payment methods. For Shopify Payments, you get a breakdown of settlement costs and fees. Plus, a clearing account is set up for faster bank reconciliation.

For all third-party payment solutions that you’re using, you need to set up a clearing account for each. Clearing accounts help to keep track of payments that haven’t reached your bank account. After it’s been deposited, you will have to allocate it to the relevant clearing account to offset the balance. Need more help? Feel free to reach out to the Amaka support team.

How to set up a Shopify accounting integration

There are three setup options available for Amaka’s accounting integration. The first option is the 2-Minute Express setup for those that have basic needs. For those that have unique requirements, the Advanced setup options allows for custom mapping. Finally, the Guided setup option lets you schedule in a free onboarding call with one of our integration specialists.

As part of the setup process, you can choose what time you want the daily sync to run, your custom mapping, how you want your invoice broken down and your invoice format. To maintain your books, you’ll need to regularly reconcile payments for your Shopify store. The integration will automatically match transactions to your bank feed meaning you just have to click OK.

Can I automate my accounting for multiple sales channels?

If you’re leveraging a multichannel approach, you’ll be happy to know that you can automate your accounting with multiple sales channels. If you’re using Shopify POS, you don’t need to install any more solutions. Amaka’s Shopify accounting integrations will automatically work for both e-commerce and POS.

On top of that, if you’re using an additional sales channel such as a marketplace or a different POS system, Amaka offers a wide range of accounting integrations. For example, Amazon, Revel, Square and many more. You can connect multiple sales channels to one account in your accounting software.

Key takeaways on managing multiple payment methods

Offering multiple payment options on your Shopify store can come with some extra administrative work, especially at the beginning. Fortunately, by taking the steps in this article, you can automate a lot of your bookkeeping and accounting tasks. Not only are you saving a tonne of time, you can rest assured that your financial data is always accurate and timely.

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