The deposits you receive from Amazon aren’t your gross sales. They’re what remains after Amazon deducts fees, refunds, advertising costs, and sometimes holds reserves. The number hitting your bank account has already been reduced by everything Amazon takes before sending you the balance.

Amazon’s fee structure creates most of the gap. Referral fees typically run 8% to 15% depending on your product category. FBA fees cover picking, packing, and shipping if you use fulfillment by Amazon. Storage fees add up, especially during Q4 when rates increase. If you’re running Sponsored Products or other advertising, those costs come out of your settlement too. By the time Amazon calculates your payout, a significant portion of your gross sales has disappeared into various fee buckets.

Refunds create another layer of mismatch. When a customer returns an item, Amazon refunds them immediately but deducts it from your next settlement. The original sale might have been processed in a previous period, so you’re seeing the refund hit a different deposit than where the sale landed. This makes period-over-period comparisons confusing if you’re only looking at deposits.

Timing differences also contribute. Amazon pays sellers on a two-week settlement cycle for most accounts. Sales happening near the end of one settlement period might not appear until the next payout. Your sales dashboard shows real-time transactions, but deposits reflect settlements that don’t align neatly with those dates.

Amazon occasionally holds reserves, especially for newer seller accounts or during high-refund periods. If this is happening, you’ll see a reserve balance in your Payments section. That money exists but won’t hit your bank until Amazon releases it, sometimes weeks or months later.

To reconcile properly, use Amazon’s Settlement Reports rather than the Business Reports. Settlement reports show exactly what was paid, what was deducted, and why. This is the data that matches your deposits. The business reports are useful for tracking sales performance but don’t reflect what actually transfers to your bank.

For e-commerce businesses selling on Amazon, this reconciliation work needs to happen every settlement period. Many sellers spend hours trying to match deposits manually when the real solution is setting up proper accounting processes that account for Amazon’s structure from the start.

If your books have been tracking gross sales while your bank shows net deposits, the discrepancy compounds over time. Scottsdale bookkeeping services that understand Amazon selling can set up your chart of accounts to track gross sales, fees by category, and net deposits separately. This gives you accurate profitability data and books that actually reconcile without a scramble at year end.