How do I track Amazon fees and FBA costs?
The tricky part with Amazon bookkeeping is that you don’t get paid per transaction. Amazon sends you a lump sum deposit every two weeks that mixes together your sales revenue, refunds, and dozens of different fee categories. Without breaking this down, your books just show random deposits that tell you nothing about actual profitability.
The cleanest approach is using an integration app like A2X, Link My Books, or Webgility. These tools connect to your Amazon Seller Central account and pull settlement data directly into QuickBooks. Instead of one confusing deposit, you get journal entries that properly separate revenue, refunds, referral fees, FBA fees, storage fees, advertising costs, and everything else Amazon deducts before paying you. For e-commerce sellers doing any real volume, this automation pays for itself quickly.
If you’re doing it manually, download your settlement reports from Seller Central and categorize each line item. This works for low-volume sellers but becomes unsustainable as you scale. The time spent manually sorting hundreds of transactions each month usually costs more than the $20-50/month for automation software.
Set up separate expense accounts for each major fee type. At minimum, you want to track referral fees (the percentage Amazon takes on each sale), FBA fulfillment fees (picking, packing, and shipping), storage fees (monthly and long-term), advertising costs (PPC campaigns), and removal or disposal fees. Lumping everything into a single “Amazon fees” account means you can’t see which costs are eating your margins.
FBA inbound placement fees are newer and often missed. If you’re sending inventory to Amazon and not tracking what they charge to distribute it across warehouses, you’re underestimating your landed cost per unit. Same with labeling fees if Amazon is prepping your products. These smaller fees add up and should be tracked separately.
The goal isn’t just clean books. It’s understanding what each product actually costs to sell through Amazon. When you can see that a product has a 15% referral fee, $4.50 FBA fee, and 6% going to advertising, you know whether the margins make sense. Without that breakdown, you’re guessing at profitability instead of measuring it.
Reconcile your Amazon deposits to your bank account regularly. The deposit amount should match what the settlement report shows after all fees and refunds. Discrepancies usually mean a settlement got split across periods or there’s a fee you didn’t account for. Catching these early is much easier than sorting through months of mismatches at year end.
If you’re selling on multiple platforms like Shopify or Walmart alongside Amazon, each channel needs the same treatment. Different platforms have different fee structures, and you need to see profitability by channel to make smart decisions about where to invest your advertising and inventory dollars.
Amazon’s fee structure is complex and changes regularly. Working with an Andover, MA bookkeeping service that knows Seller Central reports and common integration tools means your books get set up correctly from the start. You’ll catch issues early instead of discovering margin problems or miscategorized fees during tax prep.
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