Amazon FBA bookkeeping: settlements, fees, inventory and sales tax

Amazon FBA bookkeeping means recording each Amazon settlement as gross sales, refunds, fees and reimbursements rather than as a single bank deposit, tracking FBA inventory as an asset until it sells, and separating the sales tax Amazon collects and remits from the tax you still owe. Done monthly, it turns a net payout into a margin you can trust.

What makes Amazon FBA bookkeeping different?

Amazon does not pay you for each order. It schedules settlements itself, typically every two weeks, and deposits the net amount after fees, refunds, advertising charges and any reserve it holds back (Amazon, 2026). A seller who books that deposit as sales understates revenue, hides fees and makes margins look better than they are.

The second difference is the number of moving parts. A single settlement file carries dozens of amount descriptions, from referral commissions to aged inventory surcharges. Referral fees alone are 15% of the sale price in most categories and 8% in a few, such as computers and consumer electronics, with a $0.30 minimum in most categories (Amazon, 2026). FBA fulfillment fees rose by an average of $0.08 per unit from January 15, 2026 (Amazon Selling Partners, 2025).

The third difference is inventory. Stock sits in Amazon warehouses, in transit, at a prep center and sometimes still at a supplier. Lost and damaged units get reimbursed weeks later. Without a monthly count, cost of goods sold drifts and the profit and loss statement stops meaning anything.

What is inside an Amazon settlement report?

Every settlement has a settlement ID, a start and end date, a deposit date and a total amount. Below that sit line items, each tagged with a transaction type, an amount type and an amount description (Amazon SP-API documentation, 2026). The table groups the common lines and shows where each belongs in the books.

The sum of every line equals the deposit. That is the test: if your posted entry does not tie to the deposit on the bank feed to the cent, a line is missing or mapped twice. Our settlement report glossary entry walks through a full example.

How do you record a settlement in QuickBooks Online or Xero?

There are two workable methods. The manual method posts one journal entry or sales receipt per settlement, with each line group above going to its own account and the net to an Amazon clearing account. When the deposit lands, you match it against the clearing account, which should return to zero.

The automated method uses a connector such as A2X or Link My Books. These pull settlements from Amazon Seller Central, summarize them by line group and post an invoice or journal to your ledger. When a settlement crosses month-end, A2X splits it into two entries and carries the first month’s balance forward so sales and fees land in the month they happened (A2X Support, 2026).

Automation does not remove the bookkeeper. Someone still has to map new amount descriptions when Amazon adds a fee type, review the posted summaries, book the reserve movement and reconcile the clearing account every month. That review is the core of our payment processor reconciliation service, and our ReconBot workflow logs every exception until it is cleared.

How should FBA inventory and cost of goods sold be tracked?

Inventory is an asset until the unit sells. Record purchases at landed cost: the supplier price plus inbound freight, duties, prep and inbound placement charges. When a unit sells, move its landed cost from inventory to cost of goods sold. Keep a landed-cost sheet per SKU and update it when freight or duty rates change, because a stale unit cost quietly moves profit between months.

Small sellers usually run a periodic method. At month-end, pull the Inventory Ledger report in Seller Central, which shows opening units, receipts, orders, returns, adjustments, removals and the closing balance. Multiply closing units by landed cost, adjust the inventory account to that figure, and the difference is the month’s cost of goods sold. Add stock in transit and at any prep center separately.

Reimbursements for lost or damaged units are not free money. Remove the units from inventory at cost and book the reimbursement against the same account; anything above cost is other income. Reserves held by Amazon are a receivable, not inventory and not revenue. Our ecommerce accounting service runs this count every month for the sellers described on our ecommerce industry page.

How does marketplace facilitator sales tax work for Amazon sellers?

Every US state with a sales tax now has a marketplace facilitator law, which shifts collection and remittance on marketplace orders to the marketplace (TaxJar, 2026). Amazon calculates, collects and remits the tax on orders it facilitates and shows it in the settlement as tax collected and tax withheld (Amazon, 2026). The two lines net to zero, so the tax is neither your revenue nor your liability.

That does not end your sales tax work. A facilitator only covers sales made through its platform; sales from your own website or a wholesale channel are still yours to collect and file (TaxJar, 2026). Many states expect registered sellers to keep filing, often a zero return, and FBA stock stored in a state can create nexus for your non-Amazon sales. Some local taxes fall outside facilitator rules.

The bookkeeping rule is simple. Map facilitator tax lines to a pass-through account that must net to zero each month, and keep a separate liability account for tax you collect on other channels. TaxJar or Avalara can file the returns; our sales tax reconciliation service ties both accounts out before filing. Sellers in the UK, Canada and Australia face similar deemed-supplier rules for VAT and GST and should confirm their registration status on the marketplace’s tax pages.

Why does Form 1099-K not match your bank deposits?

Amazon issues Form 1099-K when gross payments exceed $20,000 and the transaction count exceeds 200 in a calendar year (IRS, 2026). The form reports the gross amount of reportable transactions without regard to fees, refunds, credits, discounts or shipping (IRS, 2026). Your deposits are net of all of those, plus reserves.

Keep a one-page reconciliation: gross sales per settlement summaries, less refunds, less fees, less advertising, plus reimbursements, plus or minus reserve movement, equals deposits. When the 1099-K arrives, its gross figure should match the first line, give or take shipping and tax included in gross. A preparer who receives that page files with confidence instead of guessing.

What does a monthly Amazon FBA close look like?

1. Pull every settlement with an end date in the month and confirm each posted summary ties to its deposit.
2. Reconcile the Amazon clearing account to zero and the reserve account to the last settlement.
3. Review the fee mapping for any new amount description and map it before posting.
4. Count inventory from the Inventory Ledger, add in-transit stock, and post cost of goods sold.
5. Reconcile facilitator tax lines to zero and prepare returns where you are registered.
6. Match advertising invoices to the advertising charges in settlements.
7. Reconcile the bank, then review margin by product line before sending reports.

A dedicated accountant working inside your QuickBooks Online or Xero file can run this close for you, with a backup and a team lead reviewing every month. Pricing depends on volume and scope, so we send a custom quote within 1 business day.

Sources

• Amazon Selling Partner API documentation, Settlement reports: developer-docs.amazon.com
• Amazon, Selling plans and referral fees by category: sell.amazon.com
• Amazon Selling Partners, 2026 updates to US referral and FBA fees: sellingpartners.aboutamazon.com
• Amazon, Marketplace Tax Collection: amazon.com
• TaxJar, Marketplace facilitator laws explained: taxjar.com
• A2X Support, Why A2X splits settlements at month-end: support.a2xaccounting.com
• IRS, Instructions for Form 1099-K: irs.gov
• indinero, How much does outsourced bookkeeping cost in 2026?: indinero.com