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The Best Bookkeeping Software For eCommerce Businesses

accounting ecommerce bookkeeping
The Best Bookkeeping Software For eCommerce Businesses - Ecommerce bookkeeper UK

When it comes to growing an ecommerce business, up to date financials are essential... and of course being online savvy you should naturally be looking to cloud accounting software for all your bookkeeping needs.  There are quite a few different software options to help you with bookkeeping for ecommerce businesses. Each one has its own strengths and weaknesses, so picking between them can be hard. Let’s take a quick look at some of the big ones, to see what they can do for you.


In our professional opinion, Xero is one of the best bookkeeping tools out there. We’ve worked extensively with it for a long time, and we are a certified specialist and partner on the platform. All of our clients are using Xero to manage and scale up their businesses and it works brilliantly.

Not only does Xero have full integration with popular eCommerce platforms like Shopify and Woocommerce, but it's also based in the cloud and accepts integtrations from various global marketplaces to speed up transaction recording. If you ever ask us for a single recommendation, then this is definitely the platform we will direct you to.

We love how in Xero it's easily to reconcile Amazon sales - Xero helps you reconcile all your Fulfillment by Amazon (FBA) transactions with your bank statements easily each day using the matches suggested by Xero. It also integrated with your Amazon Seller Central account to manage your cash flow and view cash flow predictions.

For eCommerce sellers one of the most challenging areas is Inventory management.  Use Xero for simple inventory management, or else connect to a third-party inventory management app like DEAR for automatic syncing of details.

Overall one of the most powerful features of Xero is the third-party App ecosystem which sits around it, which allows you to add on and integrate Xero with pretty much anything - our favourites are cashflow forecasting app Fluidly and Dext (receipt bank) to speed up data entry - but there are so many more with functionality that ranges from handy time tracking apps that can link to payroll through to detailed analytics and reporting apps. 



QuickBooks is probably the best bookkeeping software out there for payroll bookkeeping and it's good on inventory management too. You can integrate your Shopify site with QuickBooks, which will then automatically update orders, customers, shipping, and inventory.

You can also use QuickBooks for a variety of e-commerce order information, such as batch journal entries, granular order information, and syncing up with different marketplaces like Amazon or Etsy. It’s a pretty flexible package for first time eCommerce traders.


FreshBooks is another good bookkeeping software that you could also take a look at if you are a startup looking to master bookkeeping for yourself. It's DIY-er friendly. This is a good cloud bookkeeping software that helps you to manage your Shopify orders based on three different criteria, the item, the payment and the invoice.

You can also use your Shopify inventory as the single source of truth for all your inventory management, as it automatically sync's and updates information based on new orders and sales. It’s pretty helpful on that basis alone because inventory management can be a pain for new businesses.

What Platform Is Best?

It depends!  But we are naturally going to say Xero for ease of use and ability to grow with you. 

In all honesty when looking at all the cloud software accounting platforms, it’s difficult to say that there is one true platform that is better than all the others - they all have their own unique strengths and weaknesses. The most important thing is you choose one and just get going!  Don't labour over the decision because you can always change it later. Far more important to be concentrating on driving sales, getting your business growing and cash coming in. 

We personally recommend Xero as the best general bookkeeping software for our client base as we find it super easy to use, we love the APPs(!) and it has the deep capacity and scope to scale up with you as your business grows... but of course other business owners do their bookkeeping work just as accurately with other platforms.

In terms of Functionally, it depends on what it is you’re trying to accomplish, because every platform does something a little bit different.

If you’re not interested in doing your own bookkeeping at all, then you can simply outsource all of your bookkeeping tasks to a qualified professional like us, and that professional bookkeeper will guide you on their preferred platform and help you get it set up for your business.  But if you really want to DIY the best thing to do is review what is available, take the free trials, dig in and really test it and see which platform you personally find easiest to get along with. 

If you really just can't decide, we'd say start with Xero's basic plan to just get you going - it has everything you need as a small start up and you really can't go wrong or break it, which is very reassuring for most new business owners! 


Make It Happen In Your Business

There are plenty of different bookkeeping platforms out there, so it’s important to review the major cloud accounting software options available to you. Your choice will depend on how much you want to do for yourself, and how fast you want to grow - these things will inform your need for a more or less sophisticated bookkeeping software.

We personally will always recommend the combination of using Xero for your cloud accounting software and outsourcing your bookkeeping to a professional because quite simply it frees up your precious time as Founder and CEO, to focus on more important things like growing your business and getting sales! ... but it’s always up to you as the business owner.

Regardless of which software you go for, make sure you pick something that works with the cloud. Cloud accounting based bookkeeping is vital in today's business environment and means you can access your books online, from wherever you are in the world. If you’re a business that has staff working both from home and on site, this is particularly helpful.


Next Steps

  • Review the major cloud accounting software packages that are available to you and take up the offers of any free trials. 
  • Talk to a professional bookkeeper and accountant to discover what they would recommend for your type of business and volumes of transactions. 
  • If you would like our help with setting up and training in your Xero accounting software package then please contact us to find out how we can help you. 
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