What's the best bookkeeping software for Amazon sellers?
QuickBooks Online or Xero both work for Amazon sellers. The accounting software itself matters less than how you get Amazon data into it. Amazon’s settlement reports are complicated, and trying to manually reconcile deposits against individual sales creates a mess quickly.
Amazon doesn’t pay you per sale. They bundle two weeks of sales, refunds, fees, shipping costs, and FBA charges into a single deposit. Looking at a $4,287 deposit in your bank account tells you almost nothing about what actually happened. Without proper parsing, your books become a jumble of unreconciled transactions that nobody can make sense of.
The solution is an integration tool that sits between Amazon and your accounting software. A2X and Link My Books are the two most common. They pull your Amazon settlement data, break it into proper categories, and create journal entries that post to QuickBooks or Xero. Sales go to revenue, fees go to expenses, refunds go where they belong.
These integrations handle what manual bookkeeping can’t. They match the exact deposit amount to the proper breakdown of revenue, cost of goods sold, Amazon fees, FBA fulfillment charges, advertising costs, and refunds. Your bank reconciliation works because the numbers actually match.
Inventory tracking adds another layer. If you’re using FBA, you need to track inventory sent to Amazon warehouses along with what’s been sold, returned, or marked as damaged. QuickBooks handles inventory with additional setup, though some sellers use separate inventory management tools that sync with their accounting software. Working with a Scottsdale bookkeeper who understands these integrations saves time compared to figuring it out yourself.
The choice between QuickBooks Online and Xero comes down to preference. Both integrate with A2X and Link My Books. Both handle e-commerce accounting when configured correctly. The difference is having the right integrations running and a chart of accounts structured for Amazon selling. Generic bookkeeping setup without e-commerce-specific configuration creates more problems than it solves.
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