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Why your Amazon deposit doesn’t match your sales
September Amazon settlement
| Gross product sales | 39,656.50 |
|---|---|
| Refunds | (1,236.50) |
| Net sales | 38,420.00 |
| Referral fees | (4,610.20) |
| FBA fulfillment fees | (2,371.85) |
| FBA storage fees | (221.35) |
| Reserve held back | (412.75) |
| Deposit received in bank | 30,803.85 |
| Between gross sales and the deposit | 8,852.65 |
SAMPLE · DEMO STORE · NOT A CLIENT
Amazon does not send you each sale as it happens. It pays out in disbursements, which Intuit describes as typically covering sales over a 14-day period.[1] Before the money leaves Amazon, refunds and Amazon’s fees have already been taken out, and some money can be held back as a reserve. Amazon describes account-level reserves as funds held back to cover potential obligations such as refunds, claims or chargebacks, released once the underlying issue is resolved.[3]
In the example, the demo store’s September Amazon sales were 39,656.50 gross. After 1,236.50 of refunds, 7,203.40 of fees and a 412.75 increase in the reserve, 30,803.85 reached the bank. The 8,852.65 gap is not missing money: every dollar of it is a refund, a fee or cash Amazon is still holding for you.
The same gap is why a Form 1099-K rarely matches deposits: see why your 1099-K doesn’t match your sales.
The common mistake: recording the deposit as sales
The quickest way to book Amazon is to categorize each deposit as income. It balances the bank, and it gets three things wrong at once:
- 01
Sales are understated
The demo store would show 30,803.85 of Amazon sales instead of 38,420.00 net, 7,616.15 short.
- 02
Fees disappear
7,203.40 of Amazon fees, 18.7% of net Amazon sales, never appear as an expense, so you cannot see what selling on Amazon costs.
- 03
The margin looks better than it is
Gross profit after fees on Amazon was 17,401.00, a 45.3% margin. Booked from the deposit, the same month shows 55.1%, because the fees are hidden inside a smaller sales figure.
- 04
The reserve goes missing
The 412.75 Amazon still holds is your money. Booked from the deposit, it is neither a sale nor an asset, so profit is 412.75 too low until it is paid out.
What a settlement contains
A settlement already holds everything the books need. The demo store’s September Amazon settlement contains 39,656.50 of gross sales, 1,236.50 of refunds (so net sales of 38,420.00), 7,203.40 of referral, fulfillment and storage fees, and a 412.75 reserve that is still your money and belongs on the balance sheet as an asset. Recorded as one entry, with each of those parts on its own line, the settlement totals exactly the 30,803.85 deposit, so the bank ties and your sales and fees are both visible.
Two things a settlement does not tell you on its own. A payout that spans two months has to be split so each month carries its own sales and fees. And it shows what sold, not what it cost you: see cost of goods sold for an online store.
Summary per settlement or order-level sync
There are two common ways to get there, and both can produce correct books. The choice is about how much detail you want inside QuickBooks.
| Point | Summary per settlement | Order-level sync |
|---|---|---|
| What lands in QuickBooks | One journal or invoice per payout, a line per type: sales, refunds, each fee, reserve | Each sale and refund as its own transaction, with item details, plus the payouts |
| Ties to the bank deposit | The entry totals the deposit | Payouts are recorded to the bank account you choose |
| Suits | High order volume; a ledger that stays readable | Seeing sales by item and by day inside QuickBooks |
| Examples | A2X, Link My Books | Intuit’s Amazon Connector by QuickBooks |
Summary per settlement. A2X sends each settlement to QuickBooks Online as a journal, and splits a settlement that crosses month end into one journal per month; the journal is then matched to the deposit in QuickBooks banking.[4] Link My Books generates a summary invoice for each Amazon payout, broken down into sales, refunds, fees and tax, which it says matches the deposit received in the bank.[5]
Order-level sync. Intuit’s Amazon Connector by QuickBooks imports transactions from Seller Central into QuickBooks Online, with fees, gross amount, shipping, discounts, taxes and products for each payment, refunds as separate transactions, and payouts to the bank account you set.[1] Intuit says the current app brings sales in right away with item-level details and can import up to 12 months of history.[1][2]
Done correctly, either route leaves the Amazon entries for each payout adding up to the deposit, to the cent.
When to get help
If your Amazon deposits have been booked as sales, or the books and Seller Central no longer agree, our Amazon seller accounting rebuilds each settlement into sales, refunds, fees and reserve, ties every payout to the bank, and adds cost of goods sold, so your Amazon margin is real each month. If several months are affected, start with catching up on behind books.
[[FILL]]
Reviewed [[FILL: date]] by [[FILL: reviewer name]], [[FILL: credential, exactly as held]]
Written by [[FILL: author name]], e-commerce bookkeeper
Last updated [[FILL: date]] · Re-checked: yearly, or when a source changes
Sources
- QuickBooks Online Help: Connect Amazon Seller Central to QuickBooks (Intuit, updated 4 Aug 2026) fetched 7 Oct 2026
- QuickBooks Online Help: Migrate your Amazon integration in QuickBooks Online (Intuit) fetched 7 Oct 2026
- Amazon Seller Forums: Understanding Account Level Reserves (post by Amazon staff) fetched 7 Oct 2026
- A2X Help: Where do settlements go when A2X sends them to QuickBooks Online? fetched 7 Oct 2026
- Link My Books: Amazon QuickBooks integration fetched 7 Oct 2026
General information about bookkeeping, not tax or legal advice for your situation.
How this answer was written, sourced and reviewed: editorial policy.