Why your Amazon deposit does not match your sales

You sold 10,800 dollars of product, but Amazon deposited 6,550 dollars into your bank account. If you record that deposit as sales, your books are wrong before you even start, and nothing reconciles. This is the single most common Amazon bookkeeping problem, and the reason is simple once you see it: one Amazon payout is not one number. It is dozens of separate line items bundled into a single bank transfer.

Here is what is actually inside that gap, why booking the deposit as a lump sum breaks your books, and the clean method to reconcile any settlement in QuickBooks or Xero.

What is hiding inside one payout

Every Amazon Settlement report (the Flat File V2) breaks the payout into typed line items. A payout can contain any of these:

• Product sales: the item price, shipping and gift wrap the buyer paid.
• Selling fees: referral fees, and per-item fees on some marketplaces.
• Fulfilment fees: FBA pick, pack, weight and inbound charges.
• Storage and service fees: monthly storage, the Professional plan subscription, and similar recurring charges.
• Refunds: returned item price and the fees that reverse with them.
• Advertising: Sponsored Products and Brands, but only when the spend was billed to your payout rather than a card.
• Marketplace-collected tax: sales tax or VAT that Amazon collects and often remits itself.
• Reserves: money Amazon holds back this statement and releases in a later one.

Add all of that together and you get the net deposit. Sales is only the top line. Everything below it explains the difference between what you sold and what landed in the bank.

The worked example

Take the 10,800 dollars of sales and the 6,550 dollar deposit from the top of this page. Here is the whole gap, itemized:

The 4,250 dollar difference is not missing money. It is 4,250 dollars of expenses that Amazon already deducted before paying you. If you book only the 6,550 dollar deposit as sales, you understate revenue by 4,250, you record none of the fees as expenses, and your profit and loss statement is wrong in both directions at once.

The wrong way, and why it fails

The tempting shortcut is to categorize the bank deposit straight to a Sales account. It is fast, and it is wrong for three reasons:

1. Revenue is understated. Your real sales were 10,800, not 6,550.
2. Every fee disappears. Referral, FBA and storage costs never hit your expenses, so you cannot see what Amazon is really charging you.
3. Tax and margin break. Sales tax collected is buried, and per-SKU margin becomes impossible because the costs are invisible.

The books might still "balance" in the sense that the bank matches, but they do not tell the truth. That is the difference between tied out and correct.

The right way: a clearing account

The clean method used by ecommerce bookkeepers is a clearing account. It separates the accounting for the settlement from the timing of the actual bank transfer. It takes three steps.

1. Create an Amazon Clearing account

In QuickBooks or Xero, add a bank-type (or current asset) account called Amazon Clearing. This is a holding account, not your real bank.

2. Post one journal per settlement, split into its real parts

For each settlement period, post a journal entry that breaks the payout into categories, so debits equal credits and the entry nets to the payout amount:

Now revenue is right, every fee is booked as an expense, and the clearing account holds the 6,550 dollars that is about to arrive.

3. Match the bank deposit as a transfer

When the 6,550 dollars actually lands in your real bank account, record it as a transfer from Amazon Clearing to your bank. The clearing account returns to zero. If it does not, something in the split is off, which is exactly the signal you want.

The two traps that still catch people

Timing: the settlement period is not the sale period

A settlement can include refunds for sales made in an earlier period, and reserves that release in a later one. A refund posted this period does not mean the sale happened this period. Keep the refund in the current settlement for the books, but do not let it distort the current period's per-SKU margin. Reserves are not income or expense at all, they are a balance Amazon is holding, so they belong in their own account and must stay out of profit.

Unknown line types: never guess

Amazon adds new fee codes regularly, and the report uses names like Principal, Commission, RefundCommission and MarketplaceFacilitatorVAT that are not self-explanatory. If a tool silently forces an unrecognized line into some category, your books look clean and are quietly wrong. The safe habit is to flag anything you do not recognize and map it deliberately. There is a plain-English reference for every one of these codes and where it belongs on the Amazon settlement fee types glossary.

Doing it without the manual journal

The method above is correct whether you do it by hand or not. If you would rather not build the split every month, that is exactly what SkuSum does. It reads your settlement file locally in your browser, with nothing uploaded and no Amazon login, and outputs a balanced QuickBooks or Xero journal like the one above, plus a per-SKU profit view so you can see which products actually make money after fees, ads and cost of goods. Unknown line types are flagged for review instead of guessed, and the mapping is documented line by line. It is validated against 161,344 real settlement lines from US, UK, German and Indian sellers, with every line classified.