6 Best Accounting Software Picks for Ecommerce Companies


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Accounting software for eCommerce can be different from what you would normally expect to use at a brick-and-mortar store.


The general functions of online retail account software are similar, but there are key features that appeal to the eCommerce business owner. 


Whether looking for the best eCommerce accounting software for drop shipping, for selling on Amazon, for FBA, for DTC, or for private label, you’re in the right place.


My name is Connor Gillivan. I’ve been an Entrepreneur for 10+ years. My first business sold 8 figures on Amazon and I wish we had taken our accounting and bookkeeping more seriously.


With my 2nd business, FreeUp, I helped 1,000s of eCommerce business owners hire freelancers from around the world.


It’s with FreeUp that my business partner and I got our bookkeeping and accounting dialed in. It helped us to scaled to 8 figures in yearly revenue and exit the business in 2019.


Here’s what we think is the best accounting software for eCommerce. This applies for Amazon sellers, Shopify store owners, WooCommerce stores, Etsy sellers, Ebay sellers, and any other eCommerce platform. 


1. QuickBooks Online


A screenshot of the QuickBooks Online website home page.




Quickbooks online is one of the most well-known bookkeeping and accounting software tools used by thousands of industry professionals. They use the standard double-entry method of bookkeeping. While they cater to smaller businesses, large corporations can benefit from their services. So, whether you are just starting out or are an established business, this tool is flexible and can be tailored to fit your specific needs. 




Some of their offerings include cash flow tracking, invoice and payments, receipt capture, tax preparation services, tax penalty protection, a variety of financial reports, and bill management for the lower tiers. They also include dedicated accounting teams, workflow automations, data backups, Excel integrations, and access to exclusive apps for the highest tier. Regardless of the tier, you do get organized data and access to unlimited customer support. 


Because it is an online service, you don’t have to go through any download or installation processes. This makes it incredibly easy and time-saving for business owners and their accounting teams or employees to access as long as they have a stable internet connection. Quickbooks Online gives you all the information you need right at your fingertips. 


2. Xero


A screenshot of the Xero website home page.




Xero offers cloud-based accounting and bookkeeping software solutions. The tool has more than 3 million subscribers across 180+ countries. It has risen to be one of the top cloud-based accounting software solution providers. Xero offers double-entry bookkeeping services.




Businesses that are just starting out or smaller established businesses are a good match for Xero. However, they have expanded to cater to larger businesses as well. Its ease of use is one of the reasons Xero is used by millions. Whether you are a financial expert or just the average joe that doesn’t have that much experience, you won’t have a hard time with Xero. Xero allows users to track their revenue and expenses as well as banking and invoicing online, wherever and whenever. All of your accounting information is also kept in an online database you can access conveniently whenever you need to. 


Xero is an effective tool that aims to bridge the gap between small businesses and their expert financial advisors. It is well-equipped to assist you with all of your financial management needs.


3. Wave


A screenshot of the Wave accounting software website home page.




Wave offers web-based financial management solutions catered to small businesses. They also have a mobile invoicing app that users can download. Everything from income and expense tracking to tax preparations, to professional help, Wave provides businesses with the essentials they need to ease the burden of handling finances. Not only does Wave care about simple solutions, they also care about security. With their encryption technology and PCI Level-1 certification, your bank data and credit card info are safe and sound. 




Wave’s business model gives users access to their invoicing, accounting, and banking services completely for free. You can access helpful reports, create branded invoices, and easily and quickly connect your bank and credit card with Wave without spending a cent.


You can get started right away after signing up and start tracking your cash flow via their organized smart dashboard. If you find that you need more than the base invoicing, banking, and accounting services, that’s the time you can avail of their paid offerings.


They have payment and payroll solutions and you can even hire expert help from their team of professionals. You can tap these advisors year-round. They can give personalized insights into business operations and financial trends to help guide your business to where you want it to go. 

4. A2X


A screenshot of the A2X website home page.




A2X offers accounting services specifically directed at eCommerce businesses selling on marketplaces like Amazon, Shopify, eBay, and Walmart. It’s easy to set up and you can be sure to get accurate and efficient automated accounting solutions to help your business with the challenging problem areas of eCommerce accounting. A2X alleviates the accounting and bookkeeping weight, which grants businesses the freedom to allocate their resources to other areas of growth.




With A2X, you can easily integrate with other accounting software like Quickbooks and Xero. Areas of assistance include accounting and bookkeeping, sales management help, FBA inventory, and uploading Amazon settlement transactions automatically to other accounting systems.


5. ConnectBooks


A screenshot of the ConnectBooks website home page.




Use ConnectBooks to sync all your eCommerce platform data to QuickBooks. This tool will never leave you confused about your profitability. With ConnectBooks, you don’t need to lay a finger on accounting. You’ll get the most accurate reports that coincide with QuickBooks data. You can even customize how you want this data to be viewed.




ConnectBooks allows businesses to sync their sales, fees, inventory, settlements, and all other forms of data directly to QuickBooks. If you want comprehensive real-time inventory tracking and updating, stock notifications, sales data monitoring, cost breakdowns, clear ideas about your profits and what SKUs make more or less, automated accounting, daily calculations, and more, look no further than ConnectBooks.


6. LinkMyBooks


A screenshot of the LinkMyBooks website home page.




Link My Books, as the name suggests, is for Amazon sellers and other eCommerce platform accounts to be able to link to accounting software like QuickBooks. Whether you are a seller or a leading accountant, a sole proprietor or a large business, Link My Books will save you precious time. It’s easy and fast to get started with this software. Thousands of businesses trust their solutions. If you are an online seller, Link My Books has got your eCommerce bookkeeping needs covered. 




With LinkMyBooks, VAT returns don’t have to be so daunting. Their services provide default account and VAT rate selections. Never pay more than you need to on VAT with their tax law compliant sales and fee analysis. Bustling Amazon storefronts will benefit greatly from LinkMyBooks’ automatic invoice creation. 




These online retail accounting software tools cover everything you’d need to manage your bookkeeping and accounting for your eCommerce business. 


Still can’t find accounting software for eCommerce that will fit your business? Contact us and we’ll see if we can help!


Here’s also a video sharing more eCommerce accounting options:


About EcomBalance


EcomBalance is a monthly bookkeeping service for eCommerce companies selling on Amazon, Shopify, Walmart, Etsy, etc. EcomBalance takes bookkeeping off your plate and sends you financial statements by the 15th of each month so you can understand your numbers better and make smarter growth decisions. EcomBalance also has a sister company, AccountsBalance, that caters to agencies, software companies, coaches, consultants, and other online businesses.

Want bookkeeping off your plate? We’ve got you! Get started, Speak w/ a Founder, or Schedule a Callback

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Julia Valdez

Julia Valdez is Freelance Writer and Agency Owner. She regularly writes on topics related to Business Finances, Growth, Hiring, Entrepreneurship, and more.

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