How to Account for Marketplace Payouts with a Clearing Account
In September 2025 I was on a call with a customer, working out how an Amazon fee should reach their books. Amazon had already taken the fee out of the payout, and every way we tried to post it either hid it or counted it twice. Then I said this, while thinking out loud:
“The deposit amount on your bank statement is not going to match the invoice, but it will match the invoice and the bill combined.”
That is how a marketplace payout should be booked. Sales go on one invoice. What the marketplace kept goes on one bill. The two together equal the deposit to the cent. Everything else in this guide is the detail around that: what to do when a payout crosses a month end, where held money goes, and how to tell from your own books whether it’s being done.
This is the payouts part of our ecommerce accounting standards. It’s written for a seller or their bookkeeper, on Xero or QuickBooks, with any inventory system.
What a payout actually contains
Marketplaces don’t pay you per order. On an internal call in November 2026 I put it this way: “Most sales channels they pay you not like one deposit equals one sales order. They usually pay you one deposit equals a bunch of sales orders like after a day or two days or in that case of Amazon, two weeks.”
How often each one pays, from our own channel guides:
| Channel | How it pays | Source |
|---|---|---|
| Amazon | One deposit every two weeks or so | Amazon settlement mapping guide |
| Walmart | One deposit every two weeks | Walmart settlements guide |
| Shopify Payments | A payout about six days after the sales in it | Shopify and eBay payouts guide |
| TikTok Shop | Daily statements, paid out usually once a week | TikTok Shop payouts guide |
| Temu | Once per statement period, about every two weeks, with part held back | Temu payouts guide |
Inside each deposit there are usually six kinds of money:
- Sales: the product price, plus shipping charged, sometimes tax collected, less discounts.
- Refunds and return charges.
- Fees: referral or commission, fulfillment, storage, payment processing, ads paid out of the balance.
- Reimbursements and adjustments.
- Held money: a reserve withheld this period, or one released from last period.
- Inbound costs: freight and placement fees for stock you sent in, which are part of what that stock cost you.
The bank sees one number. Your books have to see all six.
The standard: one invoice, one fee bill, matched to the deposit
Ecommerce accountants commonly work to five rules here. They don’t depend on which software posts the entries.
- One payout, one set of documents. The sales and refunds go on one invoice. The fees go on one bill. Their net is the deposit, exactly.
- Gross, never net. Revenue is what customers paid. Fees are a cost. If you record the deposit as revenue, you’ve hidden the fees inside a smaller sales number, and you can’t see your fee rate move.
- Revenue is booked once. Either each order posts its own invoice, or the payout posts the sales. Never both. This is the mistake I see most, and it has its own post.
- Split at month end. A payout that covers days in two months posts one part in each month, so each month carries its own sales and fees.
- Held money is an asset. A reserve the marketplace keeps back is money it still owes you. It is not a fee and it is not less revenue.
A worked example
These numbers are invented. Say an Amazon settlement covers October 25 to November 8:
| Line | Amount |
|---|---|
| Product sales | 12,480.00 |
| Refunds | −615.20 |
| Referral fees | −1,872.00 |
| FBA fulfillment fees | −2,310.45 |
| Deposit | 7,682.35 |
Booked the standard way, it becomes two documents:
- Sales invoice: sales 12,480.00, less refunds 615.20, for a total of 11,864.80.
- Fee bill: referral fees 1,872.00 plus fulfillment fees 2,310.45, for a total of 4,182.45.
The deposit of 7,682.35 pays the invoice and the bill together: 11,864.80 less 4,182.45. When you reconcile the bank line, you match it against both documents at once, and there is nothing left over. Your profit and loss shows 12,480.00 of sales and 4,182.45 of fees, instead of one line of 7,682.35 that tells you nothing.
Where the clearing account fits
A clearing account is a balance-sheet account that money passes through on its way somewhere else. It should come back to zero. If it doesn’t, something is missing or doubled.
There are two common ways to set up the payout itself, and both are correct:
- Through a clearing account. The payout posts as one entry: credit sales, debit fees, debit a clearing account such as “Amazon Clearing” for the net. The deposit is then a transfer from that clearing account to the bank. It’s a common setup.
- Through receivables and payables. The payout posts as an invoice and a bill. The deposit pays the invoice and the bill. The receivable and the payable play the clearing role. This is how SKU.io does it.
The test is the same either way. After the deposit, the payout’s balance is zero.
Clearing accounts also earn their keep in four places around the payout:
- Each payment processor. PayPal, Klarna, Afterpay and the rest each pay you on their own schedule. Give each one its own clearing account, so each can be reconciled to its own statement. One shared “undeposited funds” pile can’t be.
- Held money. A reserve or a negative balance sits in a clearing account until the marketplace releases it or takes it back.
- The switchover. When you move from per-order invoices to payouts, the first payouts pay orders your old setup already booked.
- Orders invoiced on their own and then paid by card through a payout, such as a wholesale order on terms. The payment clears the invoice instead of becoming a second sale.
The switchover is the one that catches people. Another invented example: your old setup booked September’s Shopify sales as they happened, to a “Shopify Payments Clearing” account. You start booking from payouts on October 1. The first October payout includes 2,140.00 of sales from September 29 and 30. If that payout posts all its sales to revenue, those 2,140.00 are revenue twice. Posted against the clearing account instead, they cancel the 2,140.00 that’s waiting there, and the account goes to zero.
Month end: one payout, two months
Back to the Amazon settlement above. It ran from October 25 to November 8. Posted whole on its own date, all of it lands in November, and October is understated.
Split by the date on each line:
| October 25–31 | November 1–8 | Total | |
|---|---|---|---|
| Sales | 5,210.00 | 7,270.00 | 12,480.00 |
| Refunds | −180.00 | −435.20 | −615.20 |
| Fees | −1,690.10 | −2,492.35 | −4,182.45 |
| Net | 3,339.90 | 4,342.45 | 7,682.35 |
The October part is dated October 31. The November part keeps the settlement date. The two parts still add up to the one deposit, so the bank line still matches.
A customer’s team once asked whether each Shopify payout could be dated on the earliest order in it. My worry was the edge case: “you pick the earliest date and let’s say the earliest date is September 30th, and then that has one or two transactions and then you have let’s say 100 transactions that are October 1st. Well, now you, you just booked your revenue in September.” A split gets both right. More on that in how Shopify payouts work.
Reserves, negative balances and deposits that never arrive
A reserve. Temu holds back part of each statement and pays it out on the next one. Our Temu guide uses this pair of statements:
| Statement | Released from last time | Sales | Withheld | Deposit |
|---|---|---|---|---|
| 09/18–10/05 | 0.00 | 189.95 | −119.00 | 70.95 |
| 10/06–10/19 | 119.00 | 0.00 | −100.00 | 19.00 |
The first statement books 189.95 of sales in full and moves 119.00 into a reserve account, an asset. The second takes the 119.00 back out and puts 100.00 in. Each invoice equals its deposit, sales are counted once, and the reserve account ends at 100.00, which is what Temu still holds. The Temu post walks through it.
A negative balance. When a TikTok Shop day ends below zero, TikTok tops it up and takes the money back from a later payout. Both sides belong in the same clearing account, so they cancel there and your sales and fees stay exact. See TikTok Shop payouts.
A settlement with no deposit. An Amazon settlement can close negative, so Amazon charges your card instead of paying you. It still posts to your books, because the refunds and fees in it happened. Only the bank transfer is missing, and someone has to confirm where the money went. That is in the Amazon settlement report post.
Inbound fees taken from the payout. Amazon deducts some inbound shipment fees, such as placement and partnered-carrier transport, straight from a payout. Those fees belong in the cost of the stock, so they become a bill on the shipment. But the payout already paid them. If that bill sits open in your payables, you owe a supplier money you don’t owe anyone.
Common mistakes
- The deposit is booked as revenue. The bank feed rule codes every Amazon deposit to “Sales”. Fees vanish and refunds net out of sales without a trace.
- Revenue is booked twice. An app posts every order to the books, and the deposits are booked as sales too. Revenue doubles, and receivables grow every month and never clear.
- The whole payout lands on its payout date. Fine for a daily payout in the middle of the month. Wrong for a two-week settlement that crosses a month end.
- The reserve is treated as a fee. Or it’s ignored, and the books never agree with the marketplace’s balance.
- Every processor shares one clearing account. Nobody can say which processor owes what, so the balance is never reconciled.
- Unmapped lines go anywhere. Marketplaces add new fee types. Without a fallback account that someone reviews each month, new lines go missing or hold the payout up.
- Every settlement is assumed to have reached the bank. A failed transfer, a settlement Amazon charged to your card, or one still in transit looks the same as a paid one until you check.
- A chart-of-accounts change rewrites closed months. You move fees to a new account and every past payout moves with it. Months you’ve already reported change under you.
How to check your own books
You can do this in one sitting with last month’s bank statement and your accounting system, or with the settlement reconciliation worksheet.
- Pick three deposits per channel, the largest ones. For each, find the documents that make it up. They should add up to the deposit with nothing left over. If you can’t find them, or they come to more, you have mistake 1 or 2.
- Read the balance of every clearing account at month end. Each should be zero, or equal to money genuinely in transit or held. If one only ever grows, something posts in and nothing posts out.
- Run receivables aging and look for marketplace orders. A marketplace pays you through payouts, so marketplace order invoices shouldn’t be waiting to be paid. Many of them, months old, is the sign of revenue booked twice.
- Compare each channel’s sales for the month with the marketplace’s own report for the same month. A payout booked on the wrong side of month end shows up here as one month high and the next low.
- Compare each reserve account with what the marketplace says it’s holding.
- List every settlement that ended in the month and confirm each has a deposit, a recorded charge, or a stated reason it has neither.
- Look at your fallback or suspense account. Anything in it is a line nobody mapped.
How SKU.io books payouts
Per payout: each sale booked once
SKU.io posts its entries to Xero or QuickBooks Online. On Amazon, Shopify, eBay, Walmart, TikTok Shop and Temu, a channel set to Per payout books each sale once, from the payout. The order’s invoice stays on the order for your records, but it posts nothing and isn’t sent to your accounting system. Amazon channels start on Per payout, including ones connected before the setting existed. Shopify stores connected now start on it too, and older Shopify stores keep the mode they had. The steps are in the payout channels and order invoices guide.
By channel
- Walmart: one sales invoice and one fee bill per settlement, adding up to the deposit to the cent, built from Walmart’s reconciliation report. New settlements arrive daily. (guide)
- TikTok Shop: one sales invoice and one fee bill per payout, equal to the deposit to the cent. The reserve and negative balance stay in a balance-sheet clearing account. Payouts are read from TikTok daily. (guide)
- Temu: each statement posts as an invoice equal to the deposit, with “Others” on a separate fee bill and the rolling reserve in a balance-sheet account. Temu shares no payout API, so you import each statement from two files downloaded from Temu Seller Center, or type it in. (guide)
- Amazon: each settlement posts as a sales invoice and a fee bill that add up to what reached your bank. (guide)
- Shopify and eBay: each payout posts as invoices and bills whose net equals the deposit. (guide)
Month end
A settlement or payout that spans two months posts one part per month, with the earlier parts dated on that month’s last day, and the parts still add up to the one deposit. Amazon, Walmart, eBay and TikTok Shop share this setting. Shopify and Temu have their own. New connections start with it on. One limit: a settlement already sent to Xero or QuickBooks keeps the shape it was sent with, and re-splitting those needs our support team. (guide)
Changing accounts without rewriting the past
Each payout mapping change starts on a date. Earlier payouts keep the accounts they posted with, and payouts on or before your hard close date are never rebuilt. On eBay and Shopify lines you can also split each sale into product, shipping, discounts and tax, which sends the tax the buyer paid to your Sales Tax account instead of revenue. (guide)
Did the money arrive?
Every Amazon settlement shows a fund transfer status: Deposited, Balance owed to Amazon, Balance charged, Awaiting fund transfer, Transfer status unknown, Nothing to transfer, or Not paid out. A “Deposit needs attention” filter lists the ones to chase, and the month-end close checks them. (guide)
Inbound fees the payout paid
Inbound fees Amazon takes from a payout become a landed-cost bill numbered AMZN-LC-, so they’re part of the shipment’s cost. When the payout’s deposit can’t settle that bill, SKU.io settles it against the payout internally. Nothing new is sent to Xero or QuickBooks, and closed periods aren’t touched. A close check flags any bill left open. (guide)
The month-end checks
The close checklist includes Payout-channel order AR cleared, which blocks the close while order invoices on a payout channel still carry a receivable their payout already booked. It also warns on Amazon settlement deposits accounted for, Amazon reserve balance reconciled and Payment clearing accounts settled. The full list is in the close checks reference.
What it won’t do
SKU.io never voids a document in your accounting system on its own. If order invoices already reached Xero or QuickBooks before you switched a channel to Per payout, a report lists them, and you void them after confirming the count. That is deliberate. It’s your ledger.
Who this isn’t for
If you sell on one channel that pays out daily, posting each deposit by hand as sales and fees is manageable, and you don’t need software for it. If that one channel is under about $1M a year, a simpler inventory app such as Zoho Inventory or inFlow beside Xero or QuickBooks fits better than SKU.io. If your bookkeeper already posts payouts with a settlement tool such as A2X and you don’t need inventory cost in the same system, keep that. The setup above earns its place when you sell on two or more marketplaces with different schedules, hold reserves, and want cost of goods and payouts to come from one system without the revenue showing up twice. More on what else an inventory system should post is in what to post to QuickBooks Online, and the product side is on the accounting page.
The rest of this series
- Amazon settlement report: one invoice, one fee bill, matched to the deposit
- How Shopify payouts work, and how to book them in Xero or QuickBooks
- Why your Shopify sales don’t match QuickBooks
- Walmart Marketplace payouts: one invoice and one fee bill per settlement
- TikTok Shop payouts: what one payout contains and how to book it
- Temu seller payouts and the reserve on the balance sheet
If you sell on more than one marketplace and want to see your own last month booked this way, book a demo and bring two deposits that never matched.