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What’s the Best eCommerce Bookkeeping Software?

By now, as an eCommerce business owner, you know how important proper bookkeeping is for your business. The thing is, it can get quite complicated, especially if you don’t have in-depth knowledge and experience of bookkeeping principles and terms. That’s where ecommerce bookkeeping software comes in.

When you use it, you’ll streamline your invoicing and billing, online payment, expense tracking, and inventory management processes. Ultimately, it gives you all the tools you need to stay on top of your business’s finances and manage it quicker and easier.

The problem is, there are so many products available on the market that it could be challenging to find the right one for your business’s specific needs and requirements.

Fortunately, we’re here to help. In this post, we’ll look at the best bookkeeping software available which will hopefully make the process of choosing the right software easier.

Why do you need bookkeeping software for your eCommerce business?

Before we look at the contenders, it’s important that we first recap why you need eCommerce bookkeeping software. There are actually a few reasons, which include:

  • Invoicing and billing. It’s simple. Before you can get paid, you’ll typically need to send invoices to your customers. Even if you don’t, invoices are a vital tool for recording your income.
  • Inventory management. For your business to be profitable, you’ll need to track your inventory and orders accurately. If you do, you’ll know when to order stock, and you’ll reduce the chances of carrying unnecessary stock which, in turn, impacts your cash flow negatively.
  • Cash flow management. When running your eCommerce business, you’ll need to ensure that you pay your suppliers and have cash in hand when you need to order stock. In addition, you’ll also need enough capital to pay your monthly expenses.
  • Financial control and planning. Bookkeeping software keeps all your business’s financial data in one place and gives you the ability to get insights into your business’s financial health at a glance. This makes it easier for you to see how profitable your business is and what its expenses are, which, in turn, makes it easier to only manage your business’s finances and plan as well.
  • Analytics. With all your financial data in one place, you’ll be able to easily analyse data which will allow you to spot trends and identify patterns in your business. This gives you the insights you need to develop and implement the necessary strategies to improve your business’s processes and make it more profitable.
  • Forecasting. With bookkeeping software, you’ll have access to a wealth of financial historical data. By analysing this data, you’ll be able to make reasonably accurate projections and forecast your business’s revenue potential at any given point in time.

Keep in mind, though, these are just some of the reasons why you need eCommerce bookkeeping software and there are many more. The key takeaway, however, is that, when you want to manage your eCommerce business’s finances effectively and efficiently, you’ll need eCommerce bookkeeping software.

Must-have features in bookkeeping software

Before we get to the best eCommerce bookkeeping software, it’s important to know what features you should look out for when choosing the right software for your business. This is especially important since eCommerce businesses have unique requirements compared to brick-and-mortar stores.

So, some of the must-have features in eCommerce bookkeeping software include:

  • Platforms. Ideally, the software should be available on various platforms. This means that you’ll be able to access your business’s data, no matter where you are. Typically, cloud-based platforms give you this ability and access to your data on any mobile device or computer.
  • Multiple users. It’s vital that the platform supports multiple users. If not, you or someone you appoint will be the only persons with access to the platform. In contrast, if the platform allows multiple users, you can authorise several people to have access to the platform, and you’ll also be able to give your accountant direct access to the platform.
  • Inventory management. As an eCommerce business, inventory management is vital. It allows you to know exactly how much stock you carry when ordering new stock and reduce the possibility of carrying unnecessary stock which could impact your cash flow.
  • Tax calculations. It’s crucial that your eCommerce bookkeeping calculate sales tax for every sale you make. It’s even better if the platform can perform all your tax tasks automatically. This gives you one less thing to worry about and saves you a lot of time and effort.
  • Integration. As an eCommerce business owner, you’ll typically use a variety of systems or platforms for things like marketing, selling, payment processing and the like. It’s therefore vital that your platform of choice fully integrate with the systems you already use. This not only ensures that you save a lot of time and effort but also that all your financial data is accurate and complete.
  • Software updates. You should always ensure that the eCommerce bookkeeping software you choose does regular software updates. In this way, you’ll ensure that the system is always stable which reduces data loss. It goes further than this, though. Regular updates also show that the platform stays up to date with technological advances and bookkeeping trends and best practices.
  • Automation. Let’s face it, when you’re running an eCommerce business, you already have a lot on your plate. It, therefore, makes sense to automate as many of your business processes as you possibly can, and bookkeeping is no exception. So, you should look for software that automates as many of your mundane and repetitive bookkeeping tasks as possible.

What’s the best eCommerce bookkeeping software?

Now that you’ve seen some of the key features an eCommerce bookkeeping software platform should have, it’s time to look at some of the best eCommerce bookkeeping software available on the market today.


QuickBooks is probably one of the most popular cloud-based bookkeeping platforms, and with good reason. It has all the features you need to manage your business’s finances and cash flow effectively and efficiently. Some of its features include invoicing, expense tracking, analytics, and the ability to connect to your business’s bank account.

It's important to note, however, that the features you’ll get depend on the pricing plan you choose. For example, the cheapest option doesn’t offer analytics, multi-currency ability, and inventory management. If you want these features, you’ll have to choose a more expensive plan. For instance, only the most expensive plan offers inventory management, a feature that is vital for any eCommerce business.


Like QuickBooks, Xero is also fairly popular. It also has an extensive feature set that gives you everything you need to manage your business’s finances and cash flow easily. Some of its features include income and expense tracking, reporting, invoicing, inventory management, and the ability to integrate with third-party services like payment processors.

A major drawback with Xero is that you’re severely limited by what you can do with the pricing plans. For instance, you’ll only be able to send 20 invoices and enter 5 bills. So, while this might be alright for a business that’s just starting, you’ll quickly outgrow its capabilities, which means you’ll have to upgrade to the more expensive plans.


FreshBooks is also relatively popular in the market. Some of its features include invoicing, expense tracking, payments, reporting, and the ability to integrate with over 100 other applications including, Gmail, Slack, Stripe, Mailchimp, PayPal, and more.

Unfortunately, as is the case with QuickBooks and Xero, you’ll be severely hampered when you choose the cheapest pricing plan. For instance, with this plan, you’ll only be able to send invoices to up to 5 customers. If you want the full range of features and the ability to invoice unlimited customers, you’ll need to look at the most expensive plans.

Accountancy Cloud

At Accountancy Cloud, we have a product offering aimed directly at eCommerce businesses. The #1 finance partner for eCommerce startups, we give you everything you need to manage your cash flow, taxes, and more. What sets us apart is that we pair our smart software with financial expertise to ensure your business’s finances are managed properly. This, in turn, saves you time and lets you focus on growing your eCommerce business.

Our platform also has extensive reporting capabilities that give you the information you need to make better decisions and reduce your risks. Moreover, our platform effortlessly integrates with all the tools you already use which places all your financial information in one place where you’ll find an accurate and up-to-date picture of your business’s financial health.

The bottom line

Hopefully, this post showed the best eCommerce bookkeeping software available today and will make your decision on finding the right software for your business easier.

So, when you’re ready to take the plunge, why not consider Accountancy Cloud? With our product developed especially for eCommerce businesses, you’ll have peace of mind knowing that you have all the tools to manage your business’s finances and cash flow easier. Ultimately, you’ll set yourself up for increased growth and can generate more revenue.

To learn more about Accountancy Cloud and how it can help you grow your business, contact us today to discuss your specific needs and requirements.

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