Amazon deposited $47,312 into your bank account last month. Your Seller Central dashboard shows $68,440 in gross sales. The $21,128 difference — 30.9% of your revenue — vanished into a maze of referral fees, FBA fulfillment fees, storage charges, advertising costs, and return processing deductions. If your bookkeeper is recording that $47,312 deposit as your revenue, every financial metric you are looking at is wrong.
Amazon FBA bookkeeping is a specialized discipline because Amazon is not just a sales channel — it is a financial intermediary that collects your money, deducts dozens of fee categories, processes returns on your behalf, and pays you on a biweekly schedule with a settlement report that reads like a spreadsheet designed by accountants who hate other accountants.
This guide covers the specific bookkeeping challenges of selling through Amazon FBA: settlement report reconciliation, fee tracking by category, inventory accounting, reimbursements, advertising cost management, and sales tax obligations. For the broader e-commerce bookkeeping picture, see our complete e-commerce seller bookkeeping guide.
The Amazon settlement report is the single most important document in your Amazon FBA bookkeeping process. Every two weeks, Amazon generates a report that details every financial transaction in that settlement period — and the net amount is what hits your bank account.
A single settlement report contains:
The challenge is that a single settlement can contain thousands of individual line items. A seller doing 500 orders per settlement period will have 500+ product sale lines, 500+ fee lines, and however many refunds, adjustments, and reimbursements occurred during the period.
Manual reconciliation process: Download the settlement report from Seller Central (Reports > Payments > Settlement). Export as a flat file. Map each transaction category to the corresponding account in your chart of accounts. Post summarized journal entries to QuickBooks. Verify the net settlement amount matches the bank deposit.
Automated reconciliation: Use A2X or Link My Books to automatically parse settlement reports and post categorized journal entries to QuickBooks or Xero. A2X breaks every settlement into revenue, fees, refunds, and other categories — matching the settlement total to the penny.
Pro Tip: Never reconcile Amazon using bank deposits alone. A single bank deposit represents an entire settlement period. Without the underlying settlement report, you cannot verify that Amazon deducted the correct fees, processed all your reimbursements, or handled refunds properly. The settlement report is your source of truth — the bank deposit is just the net result.
Amazon charges over a dozen distinct fee types, and they change their fee schedule annually (usually in January and again in June). Here is the current breakdown for 2026:
Amazon’s commission on every sale. This is a percentage of the total sale price (including item price and any shipping or gift-wrap charges).
| Category | Referral Fee % | Minimum |
|---|---|---|
| Electronics | 8% | $0.30 |
| Apparel & Accessories | 17% | $0.30 |
| Health & Personal Care | 8-15% | $0.30 |
| Home & Kitchen | 15% | $0.30 |
| Toys & Games | 15% | $0.30 |
| Grocery | 8-15% | — |
| Sports & Outdoors | 15% | $0.30 |
| Beauty | 8-15% | $0.30 |
| Books | 15% | — |
| Everything Else | 15% | $0.30 |
Bookkeeping note: Referral fees should be tracked in a dedicated expense account (not lumped with COGS). They vary by product category, so if you sell across multiple categories, your blended referral fee rate is an important metric to monitor monthly.
FBA fulfillment fees cover picking, packing, shipping, and customer service. They are calculated based on the product’s size tier and shipping weight:
| Size Tier | Shipping Weight | Fulfillment Fee (2026) |
|---|---|---|
| Small Standard | Up to 16 oz | $3.22 – $3.86 |
| Large Standard | Up to 20 lbs | $4.08 – $7.35 |
| Small Oversize | Up to 70 lbs | $9.73 + $0.42/lb over 2 lbs |
| Medium Oversize | Up to 150 lbs | $19.05 + $0.42/lb over 2 lbs |
| Large Oversize | Up to 150 lbs | $89.98 + $0.83/lb over 90 lbs |
FBA fees have increased approximately 5-8% annually over the past three years. If you have not updated your unit economics model recently, your margin calculations may be based on outdated fee assumptions.
Amazon charges monthly inventory storage fees based on the cubic footage your products occupy in FBA warehouses:
Aged inventory surcharge applies to units stored for more than 181 days:
For a seller with 3,000 units of slow-moving inventory occupying 150 cubic feet after 270 days, the aged inventory surcharge alone is $682.50 per month — on top of the regular storage fee. This is why inventory velocity is not just a supply chain metric; it is a bookkeeping metric that directly impacts your monthly expenses.
Critical: Amazon’s aged inventory surcharges can exceed the cost of the product itself. Run an Aged Inventory report monthly (Seller Central > Reports > Fulfillment > Inventory Health) and set removal orders for any inventory approaching the 181-day mark that is not selling fast enough to justify the storage costs.
Amazon handles your physical inventory — which means Amazon also loses, damages, and misplaces your inventory. Inventory reconciliation for FBA sellers involves three layers:
When you ship 1,000 units to an FBA warehouse, Amazon should receive 1,000 units. They do not always. Short-received shipments are common. Your bookkeeper should compare your shipment records (units sent) against Amazon’s receiving report (units checked in). Discrepancies above 1-2% should trigger an investigation and potentially a reimbursement claim.
Amazon classifies your inventory as sellable, unfulfillable (damaged), customer-damaged, or warehouse-damaged. Units that Amazon damages in the warehouse are eligible for reimbursement — but Amazon does not always process these automatically. Pull the Inventory Adjustments report monthly and file claims for any warehouse-damaged units not already credited.
Amazon’s inventory system count can drift from actual physical inventory. The Inventory Adjustments report shows units found or lost during Amazon’s internal audits. Large adjustments (positive or negative) should be investigated and reconciled against your accounting records.
Bookkeeping treatment: Inventory adjustments flow through your Inventory Write-Down account (5600 in the chart of accounts from our e-commerce bookkeeping guide). Do not bury these in COGS — they need to be visible as a separate line item so you can monitor the trend.
Amazon owes sellers money more often than most sellers realize. Reimbursements cover inventory lost in the warehouse, inventory damaged by Amazon, customer returns that were never received back into inventory, incorrect fee charges, and other adjustments.
Common reimbursement categories:
How to claim: Amazon has an 18-month lookback window for most reimbursement claims. Use Seller Central’s case management system or a third-party tool like GETIDA, Refund Genie, or Seller Investigators to identify and file claims systematically.
Bookkeeping treatment: Reimbursements are recorded as a reduction to marketplace fees (or as Other Income, depending on the nature of the reimbursement). They are not revenue — they are a recovery of costs Amazon should not have charged or inventory value Amazon owes you.
For most FBA sellers, unclaimed reimbursements represent 1-3% of annual revenue. On a $1M Amazon business, that is $10,000-$30,000 left on the table.
Amazon PPC (Sponsored Products, Sponsored Brands, Sponsored Display) is a mandatory expense for most sellers. Advertising costs typically run 10-25% of Amazon revenue, making it the second or third largest expense category.
Your bookkeeping system needs to capture advertising spend at the campaign level — or at minimum, the monthly total — and calculate two key metrics:
ACOS (Advertising Cost of Sale): Ad spend divided by ad-attributed revenue. An ACOS of 25% means you spent $0.25 in ads for every $1.00 in ad-attributed sales.
TACOS (Total Advertising Cost of Sale): Total ad spend divided by total revenue (including organic sales). This is the better metric because it captures the halo effect of advertising on organic rankings. A declining TACOS means your organic sales are growing faster than your ad spend.
| Metric | Calculation | Target Range |
|---|---|---|
| ACOS | Ad Spend ÷ Ad-Attributed Revenue | 15-30% (category dependent) |
| TACOS | Total Ad Spend ÷ Total Revenue | 8-15% (mature products) |
| Break-Even ACOS | Pre-Ad Profit Margin × 100 | Varies — know yours before setting bids |
Bookkeeping note: Amazon deducts advertising costs directly from your settlement. They appear as “Other Transaction Fees” in the settlement report. Your bookkeeper must extract advertising costs from the settlement and post them to the Amazon Advertising expense account — not lump them with referral fees or other marketplace fees. A2X handles this separation automatically.
Amazon collects and remits sales tax in all states with marketplace facilitator laws — which is all 46 states (plus DC and Puerto Rico) that impose sales tax. This covers the vast majority of your Amazon sales.
However, your Amazon FBA bookkeeping still needs to account for sales tax because:
Key insight: Amazon FBA inventory placement creates sales tax nexus in every state where your products are physically stored. Amazon currently operates fulfillment centers in over 40 states. Check your Inventory Placement report to see exactly where your inventory has been sent — this determines your nexus footprint. For the full state-by-state breakdown, see our e-commerce sales tax compliance guide.
Manual Amazon reconciliation is viable for sellers doing under 100 orders per month. Above that threshold, the time cost of manually parsing settlement reports exceeds the cost of automation.
A2X is the most widely used Amazon-to-QuickBooks integration tool. Here is how it works:
Critical setup decisions:
Cost: A2X starts at $19/month (Mini, up to 200 orders/month) and scales to $139/month (Unlimited). For a seller doing 2,000+ orders/month, the $139/month saves 15-20 hours of manual reconciliation time — a clear ROI.
A disciplined monthly close process ensures your Amazon FBA bookkeeping stays current and accurate. Here is the checklist:
Week 1 (1st-7th of following month):
Week 2 (8th-14th):
Week 3 (15th-21st):
When to get help: If you are doing over 1,000 orders per month and spending more than 10 hours on bookkeeping, or if your 1099-K does not reconcile to your books within 5%, it is time for a specialized e-commerce bookkeeper. Get an instant quote or learn about our Amazon seller bookkeeping services.
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