Amazon seller bookkeeping: settlements and FBA

Amazon seller bookkeeping has one source document, and it is not the bank statement. An FBA seller sells $18,400.00 of product in the first half of October and receives $9,228.31 two days after the settlement closes. The other $9,000-odd went to referral fees, fulfillment fees, storage, ads, a refund, the monthly plan and a bigger reserve than last time, and every one of those is on Amazon’s settlement report and nowhere else. A file built from deposits shows half the sales, none of the fees, and an inventory balance nobody has checked against Amazon’s warehouses.

This post works one settlement into QuickBooks Online line by line, explains reserves and why a settlement can come out negative, covers deferred transactions and month end, and sets out how to keep FBA inventory and cost of goods sold right. It is the Amazon page in our ecommerce bookkeeping series, which covers selling on several channels at once.

How Amazon pays sellers

Amazon describes its own cycle this way: “In general, Amazon settles seller accounts every two weeks. We take your beginning balance, add your sales, subtract expenses, and adjust for any refunds, then transfer payment to you after withholding an amount in reserve. The reserved amount becomes the beginning balance for your next settlement period.” After Amazon starts a transfer, “it can take up to five business days for the funds to appear in your bank account” (Amazon: how seller payments work, read October 25, 2026).

Three features of that cycle shape the books:

• Settlement periods ignore the calendar. A 14-day period can start on the 24th of one month and end on the 7th of the next, so settlements do not line up with month end.
• Sales wait before they settle. Amazon says “most transactions are deferred for some period of time before they are paid out,” and for deliveries “we typically reserve funds for seven days to give customers time to inspect their purchases.” This is the delivery date plus 7 days policy sellers call DD+7. Invoiced Amazon Business orders wait longer.
• A reserve rolls forward. Each settlement releases the last reserve and holds a new one, so the payout is never just this period’s sales less this period’s fees.

Settlement report lines and their QuickBooks accounts

Every settlement uses the same few dozen line types. Map each to an account once, and every later settlement follows the same map. Account names are the ones used across this series.

Settlement line	QuickBooks Online account	Notes
Product sales (principal)	Sales	What buyers paid for the items
Shipping and gift wrap credits	Shipping Income	What buyers paid for shipping and wrap
Promotional rebates	Discounts Given	Coupons and promotions you funded
Sales tax collected and marketplace tax withheld	Marketplace Tax Clearing, or left out	Amazon remits it; the two lines cancel
Referral fees	Marketplace Fees	Per item, by category
Professional plan, or $0.99 per item on the Individual plan	Marketplace Fees	The selling plan
FBA fulfillment fees	FBA Fees	Per unit, by size and weight
Monthly storage, aged inventory surcharge	FBA Fees	Charged on stock held in Amazon’s network
Returns processing, removal and disposal fees	FBA Fees
Inbound placement service fee	Inventory Asset, with inbound freight	Part of getting stock to where it sells; agree the treatment with your CPA and apply it every time
Refunded principal and shipping	Sales Returns and Allowances
Referral fee credited back on a refund	Marketplace Fees, as a credit	Use the amount on the report
Cost of advertising, when charged to the seller account	Advertising	Sponsored Products and similar
FBA inventory reimbursement	Inventory Shrinkage, as a credit	Against the cost of the lost or damaged units
Previous reserve released, current reserve held	Amazon Reserve	An Other Current Assets account; not income or expense
Net settlement	Amazon Clearing, then Business Checking	One deposit, one bank line

Amazon Clearing is an Other Current Assets account that stands in for what Amazon owes you. The fee names come from Amazon’s own pages. Amazon lists “an FBA fulfillment fee,” “a monthly inventory storage fee,” “a monthly aged inventory surcharge” on inventory in its fulfillment centers “for 181 days or longer,” and “an FBA disposal order fee” (Amazon: fees for selling on Amazon), and says other FBA costs “may include costs for aged inventory, returns processing, removal or disposal of inventory, and FBA inbound placement service” (Amazon FBA fees guide), both read October 25, 2026. Selling fees are the plan, $39.99 a month for Professional, and referral fees from 3% to 45% by category, with a $0.30 minimum in most categories (Amazon pricing, read October 25, 2026). Rates change; book what the report shows.

One settlement, worked

A private-label seller on FBA has a settlement from Thursday, October 1 to Wednesday, October 14, 2026. The previous settlement held back $1,200.00 in reserve. The settlement summary reads:

Amazon settlement, Oct 1 to Oct 14	Amount
Previous reserve released	1,200.00
Product sales	18,400.00
Shipping credits	350.00
Promotional rebates	−600.00
Sales tax collected	1,380.00
Marketplace facilitator tax withheld	−1,380.00
Referral fees	−2,722.50
FBA fulfillment fees	−3,960.00
Refunded principal	−540.00
Referral fee credited on the refund	64.80
Monthly storage fee for September	−410.00
Cost of advertising	−1,250.00
Professional plan	−39.99
FBA inventory reimbursement, 4 lost units	86.00
Current reserve held	−1,350.00
Transferred to the bank	9,228.31

The settlement goes into QuickBooks Online as one journal entry dated the last day of the period, and the deposit is matched from the bank feed when it arrives on Friday, October 16:

Date	Account	Debit	Credit
Oct 14	Amazon Clearing	9,228.31
Oct 14	Discounts Given	600.00
Oct 14	Marketplace Fees	2,722.50
Oct 14	Marketplace Fees	39.99
Oct 14	FBA Fees	3,960.00
Oct 14	FBA Fees	410.00
Oct 14	Sales Returns and Allowances	540.00
Oct 14	Advertising	1,250.00
Oct 14	Amazon Reserve	1,350.00
Oct 14	Sales		18,400.00
Oct 14	Shipping Income		350.00
Oct 14	Marketplace Fees		64.80
Oct 14	Inventory Shrinkage		86.00
Oct 14	Amazon Reserve		1,200.00
Oct 16	Business Checking	9,228.31
Oct 16	Amazon Clearing		9,228.31

The tax lines are left out, because they cancel and the tax was never the seller’s; the gross-up alternative is in does Etsy, eBay or Shopify collect sales tax? Amazon Clearing takes in the $9,228.31 net of the settlement and gives it straight to the bank. Amazon Reserve goes from $1,200.00 to $1,350.00, which is the reserve Amazon now holds. Sales are $18,400.00, not the $9,228.31 deposit, and every fee sits in its own account where it can be checked against the next settlement and the one after.

Splitting fees this way is what makes Amazon margins readable. In this period, referral and FBA fulfillment fees alone are 36% of product sales. Booked from the deposit, that cost would be invisible, and so would a fulfillment fee increase or a storage bill that doubled.

Why a settlement can be negative, and what reserves are

A settlement is negative when what Amazon takes out exceeds what it collected: a period of heavy refunds, a large storage or removal bill in a slow fortnight, or a reserve that rose faster than sales. Amazon says that if the account “has a negative or zero balance due to expenses or product refunds, Amazon may not initiate payment.” Every seller also registers a card as a charge method in Seller Central, and sellers report negative balances being charged to it. A charge like that arrives on the credit card feed, not the bank, and it is coded to Amazon Clearing, because it pays Amazon what the settlement said you owed.

Reserves are not a cost. Amazon calls the account-level reserve “a portion of your balance that we hold in reserve for a period of time to cover potential circumstances like refunds or chargebacks.” It is still your money, so it belongs on the balance sheet. The pair of lines on each settlement, previous reserve released and current reserve held, moves Amazon Reserve from one level to the next, as in the worked entry. Booked as fees and income instead, a reserve inflates both sides of the profit and loss by its whole amount every two weeks.

Deferred transactions and month end

Because settlements cross month end, the books need a cutoff. Two approaches work:

• Post per settlement, accrue the open days. Post each settlement as it closes, as above, and check that Amazon Reserve equals the reserve on the latest settlement. Sales and fees from the days after the last settlement closed are not in the books yet, so at month end add an entry for them from the Date Range report below, debiting Amazon Clearing, and reverse it on the first of the next month. Small sellers sometimes skip the accrual and accept the settlement date as their cutoff; that is a choice to make with your CPA, and to make the same way every month.
• Post the calendar month from the Date Range report. Amazon updated its Date Range Transaction and Summary reports by April 30, 2026, for US sellers. For periods starting January 1, 2025, they include “both transactions that have already been released to your balance, as well as transactions that are deferred,” dated by the posted date, with a column showing deferred or released and a Transaction Release Date (Amazon announcement). Amazon’s staff add that report behavior may vary by account and rollout stage, so check one month against your settlements first. That makes a calendar-month entry possible straight from Amazon’s data, with the settlement deposits clearing Amazon Clearing as they arrive and the month-end balance of Amazon Clearing plus Amazon Reserve equal to what Amazon owes you, deferred amounts included.

Pick one and keep it. Mixing the two, a monthly entry in some months and per-settlement entries in others, double counts whatever straddles the switch.

FBA inventory and cost of goods sold

Stock in an Amazon fulfillment center is still the seller’s inventory, and so is stock on its way there. It belongs in Inventory Asset at cost until it sells. The cost includes what it took to get the units to where they are sold:

• Product cost from the supplier’s invoice.
• Inbound freight and duties to bring the goods in, and the freight to send them into Amazon’s network. These are part of the units’ cost, not a shipping expense. Shipping orders out to customers is different: under FBA, Amazon does that and charges the fulfillment fee, which is an expense.
• Prep and labeling, if a third party does it before the stock goes to Amazon.

At month end, count from Amazon’s inventory reports and your own records:

Cost of Goods Sold = Beginning inventory + Purchases and landed costs − Ending inventory

• Beginning inventory, October 1: $42,000.00
• Purchases in October: $18,000.00, plus $1,400.00 of inbound freight
• Ending inventory, October 31: $37,200.00 in FBA, $6,500.00 in your own storage, $2,100.00 in a shipment not yet received by Amazon, $45,800.00 in total
• Cost of Goods Sold for October: $15,600.00

Stock in transit to Amazon is the line most often missed, because it is in neither warehouse. Leaving it out understates inventory and overstates cost of goods sold for the month.

Removals, disposals and reimbursements

• Removal to you or a 3PL. The units are still inventory; only their location changes. The removal fee goes to FBA Fees.
• Disposal. The units are gone. Move their cost from Inventory Asset to Inventory Shrinkage, and the disposal fee to FBA Fees.
• Lost or damaged in Amazon’s network. Write the units’ cost off the same way, then credit the reimbursement to Inventory Shrinkage. In the worked settlement, 4 units costing $18.00 each were lost: $72.00 comes out of Inventory Asset, and the $86.00 reimbursement leaves Inventory Shrinkage with a $14.00 credit for the period.
• Customer returns. Units Amazon puts back into sellable stock go back into inventory; unsellable ones are removed or disposed of as above.

Keeping a quantity count per SKU inside QuickBooks needs the Plus or Advanced plan and item-level sales, which usually means a connector. Most FBA sellers keep units in Amazon’s reports or an inventory app and post a monthly count adjustment instead. Both methods, and the IRC §471(c) option for small businesses, are in journal entry for inventory.

Settlement connector apps

The mapping above is what any connector automates: it reads each settlement and posts one summarized entry to QuickBooks with the lines split to your accounts. Apps built for this include A2X, Link My Books, Synder, Taxomate and Webgility, and Amazon lists accounting apps in its Selling Partner Appstore. They differ in how they handle inventory, multiple marketplaces and the calendar-month cutoff, so compare them against one real settlement you have already worked by hand. An app that posts every Amazon order as its own sales receipt, rather than one summary per settlement, fills a file with thousands of transactions and is harder to reconcile, not easier.

Whatever posts the settlements, nobody should also code the deposits to income in the bank feed. The deposit is matched to Amazon Clearing, once.

Common questions about Amazon seller accounting

How often does Amazon FBA pay?

By default, at the end of each settlement period, which Amazon says is generally every two weeks, and then up to five business days for the bank. Amazon also offers Express Payout to eligible US sellers, which it says pays out within 24 hours.

How much does Amazon take from a $100 sale?

It depends on the category and the product’s size. In a category with a 15% referral fee, $15.00 goes to the referral fee, then the FBA fulfillment fee for that size and weight, plus a share of storage and the $39.99 monthly plan. Amazon’s Revenue Calculator and the Fee Preview report in Seller Central give the figures for a specific product.

Does Amazon send a 1099-K?

Amazon issues Form 1099-K to sellers who meet the federal or state threshold, and like every platform’s form it reports gross payments, not deposits. How to tie it to the books is in why your 1099-K doesn’t match your books.

Do Amazon sellers need accrual accounting?

For management books, inventory has to be an asset either way, or margins mean nothing, and the per-settlement entry above is already close to accrual. Which method the tax return uses is a decision for your tax preparer; the cash method limits are discussed on the ecommerce bookkeeping page.

When Amazon was booked from deposits

The usual file has every settlement deposit in Sales, inventory purchases in cost of goods sold, and nothing in between. The fix is to pull every settlement for the period, post each one through Amazon Clearing with the reserve in Amazon Reserve, move the deposits already in Sales to the clearing account, and rebuild inventory from purchase records and Amazon’s inventory history. In a year already filed, do it only with your CPA. In an open year it is part of a QuickBooks cleanup.

$99per month of backlog20% off 6+ months

When to hand this off: if more than a few settlements went straight to Sales, or inventory has not been counted against Amazon’s reports since the opening balance, each settlement and each month’s inventory has to be rebuilt before margins can be trusted. A free file review counts the settlements first.