Best Accounting Software for eCommerce in 2021

We ranked Freshbooks as the best Best Accounting Software for eCommerce in 2021 in our roundup. Click here to get 50% off for 3 Months Get 30-Days free trial


Freshbooks is a small business accounting and bookkeeping software that makes running your business a breeze.

Deployed on: Cloud

Starting From: $4.5 / month


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Sage is an entry level accounting and bookkeeping software that is ideal for SMBs and businesses want to manage their cash flow.

Deployed on: Cloud

Starting From: $10 /month


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Quickbooks by Intuit

The complete accounting toolset whether you're a freelancer or a Forbes 100 company.

Deployed on: Cloud

Starting From: $4.5 /month


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NetSuite by Oracle

One of the best cloud-based financial management solutions for medium to large organizations. It integrates with all other NetSuite order management, inventory, CRM and eCommerce functions to streamline critical business processes.

Deployed on: Cloud

Starting From: $999


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Xero is a cloud-based accounting software for medium to big enterprises

Deployed on: Cloud

Starting From: $9 / month


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Buyer's Guide

With the right accounting software, store owners and e-commerce businesses can keep track of their finances, view their profit and expense statements, saving a ton of time and thereby a lot of money. These software also help you make sure that your business covers all the legal requirements and you're in good standing in case an IRS officer pays you a visit to view your books.

The following buyer's guide for best accounting software for eCommerce will cover this comprehensive topic in a lot more detail, giving you a handful of useful tips and ideas on what to look for when committing to a software that you're probably going to be using in the next couple of years.

Whether you sell locally or globally, run a small store or a big enterprise, your business simply won't be able to stay afloat without proper expense tracking and accounting. It is also required by law, as well as helping you understand where your business stands financially.

Small and medium-sized, but also globally active companies simply cannot work without proper accounting. Accounting is required and regulated by law, but it also has a very practical purpose for the business.

With good accounting, which complies with all rules and regulations, an entrepreneur always keeps track of his business. The accounting software also ensures that legal requirements are met. A good accounting software is worth its weight in gold!

What is the best accounting software for eCommerce business?

The first question you need to answer before eyeing a solution is, what features your business ultimately requires. After all, you wouldn't want to pay extra 3rd party add on fees for a function you won't even need.

It depends a bit on your industry, the size of your company, how many seats/users will have access to the dashboard, and, of course, your budget. Once you have an answer to these questions, you can pick the suitable software option. 

Large companies will usually use programs that have been customized to their requirements and require significantly more initial setup investment, while other solutions charge on pay as you go basis. The commercially available solutions are not listed here since they're mostly custom-built for the organization's specific needs.

But for medium-sized companies and small businesses, commercial solutions are often ideal and work best. They offer all important functions and can be a real help in your company's everyday operations.

Correct accounting is crucial for the success of the business, so the selection of the appropriate program must be done with appropriate care.

Costs rarely play a role, because in the end, they are all tax deductible can be declared as business expenses.


What features to look for in an accounting software for eCommerce?

Even small businesses can quickly benefit from good accounting software. No matter whether you are a business owner who is obliged to keep only one USD, or double-entry bookkeeping, you can quickly and easily record various processes within the business.

Using this data, you can quickly create financial overview statuses, which not only useful for your tax consultant, also helps your business managers understand your financials better. Profits and losses can be easily calculated with proper and clean accounting. Also the evaluation of different transactions during the fiscal year can be done much easier with a cloud-based bookkeeping software.

A good accounting software therefore has a number of important functions. The most important ones are listed below in a brief overview:


  • Double-entry bookkeeping in one software
  • Compatible with your tax office.
  • Easy to use and understand user interface
  • Maximum security - You don't want some hacker hacking into the company's servers and have access to all your financial reports.
  • Ability to overview your business' overall status, profit and loss statement, expenses, invoices and other relevant reports from a single dashboard.
  • Ability to customize
  • Auto capture of transactions from your online store.
  • Invoicing management
  • Also the dunning process is already integrated in many software packages
  • Integration with 3rd party applications.


Are there free accounting software for eCommerce?

You can find a free solution for any problem, but they're mostly restricted in terms of their ability. Some software vendors also offer demo versions of their products. This is almost always watered down version of the full software with many features are either removed, or restricted.

You can try demo versions or get your self a free trial account to give any software a go before actually committing yourself to it, but most they offer is around a month. After that, you should subscribe to full version of your choice. 

There are of course truly free desktop software you can use such as Excel for your accounting. But they're highly limited in terms of features they provide. If you're in need of a truly reliable support, flexible applications, and most importantly, all the features your business requires, you're better off subscribing to a dedicated accounting software solution. 

However, if you're running a hobby project, or maybe just starting out, we'd highly recommend Excel for simply bookkeeping entries. 


Cem Akbulut
Co-founder, 9to5Media.

Cem Akbulut is Co-founder & CEO of 9to5Media, a software research lab that provides advice, information, and tools to help businesses thrive.

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