August 16, 2022

Best Accounting Software for Shopify Sellers

Do you have a Shopify store? Do you want to know the best accounting software for your needs? If so, read on!
Best Accounting Software for Shopify Sellers
Table of contents
Best Accounting Software for Shopify Sellers

Does your business have a Shopify store? Do you want to know the best accounting software for your needs? If so, read on! This post will be discussing which accounting software is the best for your business. We'll go in depth about what each option is and how much they cost, as well as how Shopify sellers can benefit from using them.

First up, we'll talk about how you can start off using basic spreadsheets.

shopify seller accounting spreadsheet

Shopify seller accounting spreadsheet

This is a great place to start for Shopify sellers who are just getting started or who want a completely free option for their bookkeeping. We have put together a Free Shopify Seller Accounting Spreadsheet which will help you as a new Shopify seller to keep track of your sales, refunds and fees.

Of course, the spreadsheet doesn't pull the data from Shopify automatically like some of the software options we'll discuss later on, but if you are happy to manually download the required reports from Shopify and input the data yourself then it could be a good option.

The reports you'll need to download and how to filter them to find the data you need are discussed in this article.

when to move on from spreadsheets

When to move away from spreadsheets

A good rule of thumb is when you become VAT registered then it's probably time to ditch the spreadsheet and start using accounting software. The main reason for this is that to submit a VAT return to HMRC (the UK's VAT authority) you need to follow the Making Tax Digital or MTD rules.

MTD came about in 2020 and in a nutshell, it means that you have to submit your UK VAT returns via an approved software partner. The idea is that HMRC wants to be able to see the data behind the figures included on your VAT return to see that things add up essentially.

Once you're VAT registered, you should start to think about using a software provider to account for your Shopify sales.

You might also consider the switch if you find the manual process of downloading and processing the Shopify reports tedious. Most of the software options we will discuss later are pretty good value for money when you consider just how much time you will save plus they are often more accurate than doing it manually due to the lower risk of human error.

shopify seller accounting software options

Shopify Seller Accounting Software Options

For Shopify sellers who want to streamline and manage their accounts in an effective way, there are a couple of well-renowned options available.


Accounting Software

Xero is one such example which has been getting great feedback from its users since it was first launched in 2006 by Australian Tim Lucas.

Xero has a great host of built in reports meaning you can manually enter your Shopify sales and fees and then produce profit and loss reports, balance sheets and the all important VAT Returns.

You still need to manually download and enter the Shopify sales information each month with Xero but if you use an integration app such as A2X or Link My Books then that process could be completely automated too. See the integration section below for more detail.

It's MTD compliant and you can submit your VAT returns straight to HMRC from inside Xero with the click of a button.


Xero has 3 price plans available. Stater, Standard and Premium. Starter is not really suitable for most Shopify sellers as you are limited to the number of invoices and bills you can enter on it. Most Shopify sellers choose Standard with some choosing Premium, mainly those who need the added multi-currency features.

Starter - £12/month

Standard - £26/month

Premium - £33/month

All pricing is in GBP and excludes VAT.

QuickBooks Online

Accounting Software

Another established choice for Shopify sellers is QuickBooks which was launched in 1998 by Intuit Inc but now also offers its accounting services via the cloud with its QuickBooks Online product.

Similarly to Xero, QuickBooks Online is a full solution meaning that you enter all your income and expenses and it does all the hard work for you in producing reports and VAT returns.


QuickBooks Online has 3 price plans available. Simple, Essentials and Plus. Unlike Xero QuickBooks Online pricing is mainly focused on additional users. You can only add additional users on the Essentials and Plus plans. Most Shopify sellers choose Essentials with some choosing Plus, mainly those who need the added stock features.

Simple - £12

Essentials - £20

Plus - £30

All pricing is in GBP and excludes VAT.

Why choose Xero or QuickBooks Online?

Xero and QuickBooks Online are both really good tools. In fact, they are both so similar in terms of features and pricing that it's genuinely hard to choose a winner.

Pros of Xero and QuickBooks Online

  • Great support
  • Detailed reports
  • MTD compliant
  • Submit VAT returns directly to HMRC

Both platforms offer a really good solution for Shopify sellers looking to streamline their bookkeeping. Both also offer a free trial so if you're considering one or the other then the best thing to do is try them both and judge for yourself.

shopify seller bookkeeping automation apps

Shopify bookkeeping automation integrations

Assuming you now have Xero or QuickBooks, the next thing to consider is probably going to save you the most time overall. That is an integration app.

The two main players in this market are A2X Accounting and Link My Books.

These apps help you to automate your Shopify bookkeeping completely.

They hook up directly to your Shopify account and Xero or QuickBooks and form a connection between the two. But more than that, they help you to accurately account for your Shopify sales, refunds, fees and VAT completely on autopilot.

A2X Accounting Pricing

Mini - $19/month - Max 200 orders/month

Basic - $39/month - Max 500 orders/month

Pro - $69/month - Max 2,000 orders/month

Advanced - $99/month - Max 5,000 orders/month

Standard 10K - $149/month - Max 10,000 orders/month

All pricing is in USD and excludes VAT. Larger plans are also available.

Link My Books Pricing

Starter - £11/month - Max 200 orders/month

1K - £23/month - Max 1,000 orders/month

5K - £35/month - Max 5,000 orders/month

10K - £59/month - Max 10,000 orders/month

All pricing is in GBP and excludes VAT. Larger plans are also available.

Choosing between A2X and Link My Books

A2X and Link My Books are both very good at what they do. They both make your life as an Shopify seller much easier when it comes to automating your bookkeeping.

A2X supports eBay, Amazon, Shopify, Etsy and Walmart whereas Link My Books focuses on eBay, Shopify, Amazon and Etsy. That being said it can work out less expensive to use Link My Books for your eBay, Shopify, Amazon and Etsy bookkeeping and then just use A2X for Walmart standalone.

Link My Books is well renowned for having a super easy setup process with guided wizards holding your hand along the way. Being a UK based company with a great understanding of VAT they provide default account and VAT rate selections that you can simply approve which makes set up a doddle. With A2X your tax mappings must be manually selected which can be tricky if you are not sure of what you are doing.

A2X is based in New Zealand whilst Link My Books is a British company so if you are keen on backing British businesses then this may sway your choice.

Ultimately whichever you choose you will end up saving a huge chunk of time on your Shopify bookkeeping each month. Plus by getting your VAT right you might even end up saving money too as your VAT liabilities could be reduced due to correctly separating out sales which don't incur VAT such as exports, zero rated goods and marketplace VAT responsible goods. This is a common mistake that we see many sellers making before the move to using Link My Books.

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