The settlement report is your source of truth. Amazon doesn’t deposit what you sold. They deposit what you sold minus fees, refunds, FBA storage, advertising spend, and a dozen other line items. Trying to match the bank deposit to your gross sales will never work.

Download the settlement report from Seller Central for each payout period. This report breaks down exactly what made up that deposit: product sales, shipping credits, gift wrap credits, promotional rebates, selling fees, FBA fees, refunds issued, advertising costs, and any other adjustments. The net of all these components equals what hit your bank account.

Set up a clearing account in your bookkeeping software. When the settlement period closes, record the full breakdown from the report. Gross sales go to revenue. Each fee type goes to its own expense category. Refunds reduce revenue. The net amount sits in the clearing account until the deposit arrives in your bank, then you clear it out. This method keeps your books accurate and makes the bank reconciliation straightforward.

For e-commerce sellers with any real volume, manual reconciliation becomes unsustainable. Tools like A2X or Link My Books connect to your Amazon account and automatically parse settlement reports into proper journal entries in QuickBooks. They handle the complexity of splitting out dozens of fee types and matching everything to the correct accounting periods. The monthly cost pays for itself in time saved and errors avoided.

Reconcile on the same schedule Amazon pays you. If you’re on a 14-day payout cycle, reconcile every two weeks. Letting multiple pay periods stack up makes it harder to catch discrepancies and track down issues while the details are still fresh.

Watch for timing differences at month end. A sale on January 30th might not settle until February. Accrual-based sellers need to recognize that revenue in January even though the cash arrives later. The settlement report shows when transactions actually occurred, not just when they paid out.

The biggest mistake sellers make is recording just the deposit amount as revenue. That understates your actual sales and hides your true fee burden. You need to see gross sales and the real cost of selling on Amazon separately. Otherwise you can’t make informed decisions about pricing, advertising spend, or whether the platform is even profitable for you. Working with an Andover, MA bookkeeping service familiar with Amazon’s reporting can help you set up systems that capture this detail from the start.