The challenge with Amazon is that they don’t deposit your gross sales. They deposit a net amount after subtracting fees, refunds, and other adjustments. A single deposit might represent hundreds of transactions, and without breaking it apart, you’re left looking at one number that tells you nothing about where your money actually went.

Amazon charges several categories of fees. Referral fees are the percentage cut on each sale. FBA fulfillment fees cover pick, pack, and ship. Storage fees hit you monthly and spike during Q4. If you run Sponsored Products campaigns, advertising costs come out of your settlements too. Then there are smaller charges for things like removals, long-term storage penalties, and returns processing. Each of these eats into your margins differently, and you can’t optimize what you can’t measure.

The manual approach involves downloading your Settlement Report from Seller Central and breaking it down yourself in QuickBooks. Create a journal entry for each settlement that debits your bank account for the deposit amount, credits Sales for the gross amount, and debits individual expense accounts for each fee category. This works but takes real time, especially if you have multiple settlements per month across different marketplaces.

A cleaner manual method uses a clearing account. Record the gross sales and each fee type against this clearing account, then record the actual bank deposit against the same account. When everything is entered correctly, the clearing account zeros out. If it doesn’t balance, something got miscoded and you know to investigate.

The automated approach uses integration tools like A2X or Link My Books. These apps connect to your Amazon account, pull settlement data, and post properly categorized journal entries directly to QuickBooks. Setup takes an hour or two, but after that it runs with minimal intervention. For e-commerce sellers with significant volume, the monthly cost of these tools usually pays for itself in time savings.

Which approach makes sense depends on your volume and complexity. A seller with one product line doing a few settlements per month can handle it manually. Someone selling hundreds of SKUs across multiple Amazon marketplaces needs automation or a dedicated bookkeeper.

The important thing is tracking these fees consistently over time. Referral fees and FBA costs are typically your largest Amazon-specific expenses. If you’re not breaking them out, your profit margins are guesses. And when tax time comes, you want clean records showing exactly what you paid so you’re not missing legitimate deductions. If this feels overwhelming, Phoenix area bookkeeping services that understand Amazon can set up the right structure and handle it monthly.