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.
The Merrimack Valley's Trusted Accounting Partner
The Next Step:
A 15-Minute Call
Tell us about your business and what you're dealing with. We'll listen, ask a few questions, and give you a straightforward quote.
More Questions
What financial records should landlords keep?
Landlords should keep income records, expense receipts, property acquisition documents, lease agreements, and depreciation schedules. These records support tax deductions, protect you in disputes, and help track property profitability.
Read answerShould I start over with new books or fix my existing records?
In most cases, fixing your existing records is the better choice. Starting over sounds appealing but doesn't erase tax obligations or the need for historical documentation. The right answer depends on how far behind you are and what's actually wrong.
Read answerWhat is revenue recognition for software companies?
Revenue recognition determines when you record revenue in your financial statements. For software companies, the key principle is recognizing revenue when you deliver value to the customer, not when payment arrives.
Read answerHow do I handle tip reporting for restaurant employees?
Employees report tips to you monthly, and you withhold taxes through payroll. Credit card tips track automatically through your POS, but cash tips require employee reporting. Large restaurants have additional Form 8027 filing requirements.
Read answerHow do I track equipment depreciation for my medical practice?
Start with a fixed asset schedule listing every piece of equipment with purchase date, cost, useful life, and depreciation method. Record depreciation monthly or annually in your accounting software using journal entries that debit depreciation expense and credit accumulated depreciation.
Read answerWhat are the common bookkeeping mistakes dental offices make?
Dental offices commonly fail to reconcile insurance payments to EOBs, let patient AR age without follow-up, and mix personal expenses with practice accounts. These mistakes hide revenue leaks and distort profitability.
Read answer
