The challenge with Amazon FBA bookkeeping is that what Amazon deposits in your bank account isn’t your revenue. It’s the net result after Amazon takes referral fees, FBA fees, storage fees, advertising costs, and various other deductions. If you just record bank deposits as income, your books will be wrong and your profit numbers will be meaningless.

Start with the right software setup. QuickBooks Online or Xero both work for FBA businesses. The key is connecting them to Amazon properly. Manual entry from bank deposits doesn’t give you the detail you need. You’ll want an integration tool like A2X, Link My Books, or Sellerboard that pulls data from Amazon Seller Central and breaks it into proper accounting categories.

These tools translate Amazon’s Settlement Reports into journal entries. They separate gross sales, refunds, referral fees, FBA fees, storage fees, advertising spend, and other line items. Without this breakdown, you can’t see your actual margins or understand where your money is going.

Track your inventory costs carefully. Cost of goods sold is likely your biggest expense. Every unit you sell needs a landed cost that includes what you paid for the product, shipping to get it to Amazon, prep costs, and any tariffs or duties. When Amazon sells a unit, that cost should hit your books. FIFO or weighted average costing methods work depending on your products and volume.

Amazon holds your inventory across multiple warehouses. You need to reconcile what Amazon says you have against what your books show. Discrepancies happen from lost inventory, damaged goods, and customer returns in unsellable condition. Amazon’s reimbursement reports should tie back to your records.

Sales tax adds another layer. Amazon collects and remits sales tax in marketplace facilitator states, but you still need records of what was collected and where. If you sell through other channels too, your nexus obligations get more complicated.

Separate your Amazon fees in your chart of accounts. A single “Amazon Fees” expense account hides important information. When you can see referral fees, FBA fulfillment fees, storage fees, and advertising costs individually, you can make better decisions about pricing and inventory levels.

Reconcile every Amazon settlement to your bank deposit. Amazon pays every two weeks. Each settlement should match what hits your bank account. If it doesn’t, something’s wrong in your data flow.

Most FBA sellers who try to handle small business bookkeeping themselves underestimate how time-consuming proper Amazon accounting is. The integration tools help, but someone still needs to review the data, handle exceptions, and verify the numbers make sense. Getting it set up correctly from the start saves hours of cleanup later and gives you the clarity to actually know which products are making money.