The reason Amazon reconciliation is confusing is that your bank deposit doesn’t match your sales. Amazon deposits a net payout that includes your sales revenue minus selling fees, FBA fees, refunds, advertising charges, and sometimes a reserve holdback. Trying to match your total sales to bank deposits will never work because Amazon already subtracted their cut before sending you money.

The key document is your Settlement Report from Amazon Seller Central. This report shows exactly what made up each payout: product sales, shipping credits, promotional rebates, selling fees, FBA fees, refunds issued, reimbursements, and any other adjustments. When a deposit hits your bank account, the settlement report tells you what’s inside that number.

To reconcile manually, download the settlement report for the period matching your deposit. Verify the net amount on the report matches what hit your bank account. Then record the deposit broken into its components. Gross revenue goes to sales, Amazon fees go to an expense account, refunds reduce revenue. Your books now reflect actual sales and actual fees rather than just a mysterious lump sum deposit.

E-commerce businesses face an extra layer of complexity with timing. Amazon typically pays every two weeks, but the settlement period doesn’t align neatly with calendar months. A payout you receive in early July might include sales from the last two weeks of June. For accurate monthly financials, you need to adjust for this timing difference or accept that your monthly numbers will be slightly off.

Most Amazon sellers eventually use integration software like A2X or Link My Books. These tools pull your Amazon data automatically and create accurate journal entries in QuickBooks or Xero. They handle the timing, separate the fee categories, and save hours of manual work. The monthly cost pays for itself quickly if you’re doing any real volume.

A few things to avoid. Don’t record revenue when the sale happens and again when the deposit arrives because that double-counts your income. Don’t ignore the fees embedded in the payout because you need those expenses on your books to know your true margins. Don’t reconcile the bank deposit as a single entry because you lose all the detail that makes the data useful.

Getting this right matters beyond just accurate books. Understanding your actual Amazon fees as a percentage of sales, your refund rate, and your FBA costs helps you price products correctly and figure out whether Amazon is actually profitable for your business. A Scottsdale bookkeeper familiar with Amazon can set up your chart of accounts to track these metrics automatically so you can see real profitability by product or category.