5 Best Accounting Software for Amazon FBA Sellers in 2021

One fundamental area that a business must be efficient at to succeed and thrive is accounting. A business whose bookkeeping is poor will run into financial problems in the long run. Hence, every business must strive to have a quality accounting system and this includes Amazon FBA sellers.

FBA stands for Fulfillment by Amazon and it is a service provided by the online store to its sellers to help them store, package, and ship their goods. Click here to learn more about Fulfillment by Amazon.

The process of taking stock of inventory and balancing books can be somewhat overwhelming for a seller. Therefore, we have done some research and have come up with the 5 best accounting software for you as an Amazon FBA seller that will help you properly manage your finance and aid you in maximizing profits.

Without further ado, let’s get started…


Activate with QuickBooks Desktop

Activate is engineered by Alterity, Inc. and is regarded by many as the overall best account software for Amazon FBA sellers in the market.

It has enterprise resource planning and a full-featured inventory option that is perfect for established large sellers, wholesalers, as well as distributors.

The QuickBooks Desktop Pro integrated into this software allows it to meet all the needs and sales expectations of large retailers.

You will require a one-time license for both the Windows and Mac versions which doesn’t come cheap. An onboarding fee is also required. The license and the fee take care of the initial year of usage including the support as well as maintenance of the software. However, after the first year, you’ll be required to pay a yearly maintenance fee. You can opt for the free trial application before making full payments.

Since Activate is integrated with QuickBooks Desktop, you also have to make a one-time payment for the Professional version. The QuickBooks software requires an upgrade once in three years. It could also be done more frequently depending on usage.


  • Has all the features necessary to monitor inventory
  • Ease of use with Windows operating system
  • Automated cash flow, sales, target customers, and merchandise reports
  • Empowered by QuickBooks Desktop
  • Great compliance functionality for payroll tax


  • Quite expensive
  • Purchase of separate platforms (Activate and QuickBooks Desktop) required
  • QuickBooks access features limitation 


This amazon accounting software is perfect for small FBA retailers who want to still maximize profits. This software is a full accounting system for desktops. Therefore, it is best for those who don’t or can’t make use of an online or cloud version. Nevertheless, you can still get the cloud version if you prefer that.

It is very affordable and its menu system is very intuitive which makes it easier to focus on the Amazon market rather than learning how to use the application.

The perpetual license of this application compared to Activate is very affordable and has Windows and Mac Versions. You also get a trial version if you want to test out the software first.


  • Full-featured payroll, inventory, and time tracking
  • Affordable
  • Incredible banking features
  • Supports multi-user as well as multi-department
  • Great reporting features


  • Dated Windows-based interface
  • A slight learning curve
  • Remote access limitation

GoDaddy Online Bookkeeping

If you prefer a cloud-based accounting application, then allow us to recommend GoDaddy Online Bookkeeping. It allows you to carry out all the normal financial and sales tracking which is secured on the cloud.

The cost is also quite affordable as you can choose from three different levels based on your budget. These levels are “Get Paid” which is the first tier, followed by “Essentials”, and then “Premium” which is the top tier. For all tiers, you are expected to pay a subscription fee every month. The good thing is that the fee is very affordable. This software doesn’t have a trial version or period.


  • Very easy setup and usage
  • Different types of reports
  • Quite affordable
  • Direct synchronization with seller’s Amazon account
  • Mobile app for mobile accounting


  • Can be outgrown as a seller becomes more successful
  • Lacks a trial period
  • No double-entry accounting



This application was designed for small as well as mid-sized retailers. Like the GoDaddy software, it is also cloud-based. This software has several incredible features and the subscription rate per month is very appealing even to small Amazon FBA sellers.

Fetcher equally offers three tiers that the user will pay a monthly subscription fee for. The tiers are designed according to the number of sales made in a month. Hence, the “Startup” plan is for retailers with less than 2,500 monthly sales. The “Business” plan is for those who have a sale of 5,000 monthly. The last tier, the “Empire” plan has an unlimited number of sales within a month.

The software has a trial period, but you must enter a credit card number. Therefore, you have to watch the trial period closely to avoid automatic payment especially if you haven’t decided to get the full version.


  • Amazing features for new sellers
  • Different types of reports for data visualization
  • Completely cloud-based
  • Can be easily integrated into the retailer’s Amazon account
  • Can be connected to multiple accounts


  • Customer support is limited
  • Not a detailed accounting software
  • Lacks management tools for inventory

QuickBooks Online

If Fetcher is designed for small and mid-sized sellers, then QuickBooks is designed for large or enterprise sellers. This application is for those who have already made it on the online market and just need an accounting platform that will help in increasing their profits.

This software offers you a trial period of 30 days with four tiers to choose from. The price of the application is dependent on the tier features. The four tiers available are Simple Start, Essentials, Plus, and Advanced. The first two do not have an inventory management feature.


  • Amazing rich features
  • Excellent inventory control and management
  • Great mobile apps
  • Critical tracking functionality and calculation of sales tax
  • Built-in payroll options


  • Learning curve required for novices in accounting
  • Not cost-effective
  • Lacks multiple entity support


An Amazon FBA seller has no excuse when it comes to the availability of accounting software that can be used for profit maximization. With the applications we have chosen in this article, you can make your pick and grow your business to what you desire.

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