Xero & reconciliation
Eight reasons the amount Amazon paid you differs from what's in Xero — and exactly how to fix each one.
Last updated: 19 September 2026
Short answer: when an Amazon payout doesn't match Xero, it is almost always because part of the settlement report wasn't posted, was posted twice, or was posted in the wrong currency. The most common causes are Amazon's reserve, settlements that cross two months, currency conversion on non-UK marketplaces, and duplicate invoices. Post every line of the settlement report and the invoice total will equal the deposit.
Each Amazon deposit belongs to one settlement. The settlement has a start date, an end date and a total. Before hunting for a cause, confirm three things:
If all three are true and the totals still differ, work through the causes below.
Amazon can hold back part of your balance to cover possible refunds and claims. In the settlement report this appears as two lines of the type other-transaction:
If you post sales and fees but not these two lines, your invoice will be too high or too low by the net reserve movement. Fix: post both lines to a balance-sheet account (an asset such as "Amazon Reserved Balances"), not to profit and loss. They cancel out over time; they aren't income or an expense.
A settlement that runs from, say, 25 March to 8 April contains activity from both months. Some sellers post it in two parts to keep each month's figures right, then only reconcile one part against the deposit. Fix: if you split a settlement by month, carry the balance of the first part into the second through a clearing account so the two parts together equal the deposit. The simplest option is one invoice per settlement, dated when the settlement ends.
Sales on Amazon.de are settled in euros; Amazon.com in US dollars. If Amazon converts the money before paying it into a pound account, the pounds you receive won't equal the euro invoice at Xero's daily rate. Fix: post the invoice in the settlement's own currency and let Xero record the exchange difference when you reconcile it, or pay into a currency account in Xero. Don't convert the invoice to pounds yourself — you'll lose the link to the settlement.
If fees, storage or refunds exceeded sales, the settlement total is below zero and there is no deposit at all — Amazon takes the money from your card or from the next settlement. Look for lines such as Payable to Amazon, Successful charge or Failed to transfer funds. Fix: record a negative settlement as a bill from Amazon (Xero won't accept a sales invoice below zero) and match it to the card payment. See negative Amazon settlements.
Settlement reports contain dozens of transaction types, and it's easy to miss the rare ones: inventory reimbursements, liquidations, retrocharged tax (Order_Retrocharge and Refund_Retrocharge), coupon fees, Vine fees or a tiny micro-deposit Amazon used to test your bank account. Fix: add up every amount in the settlement report and compare it to the report's total. If your posted lines add up to less, the difference is the missing rows.
On orders where Amazon collects the VAT as a marketplace facilitator, the report shows the VAT charged to the buyer and then the same amount withheld again (MarketplaceFacilitatorVAT-Principal and -Shipping). If you post the VAT but not the withholding, the invoice is overstated by exactly that VAT. Fix: post both rows so they cancel. See Marketplace Facilitator VAT explained.
Switching tools, re-importing a settlement or a failed void can leave two invoices for the same settlement. Your receivables are then double what they should be and only one invoice can be matched. Fix: search Xero for the settlement ID, keep one invoice and void the other. See duplicate Amazon invoices in Xero.
Amazon's amounts are VAT-inclusive. If the invoice is set to "tax exclusive", Xero adds VAT on top of every line and the total comes out about 20% too high on standard-rated lines. Fix: set the invoice to "tax inclusive" so Xero extracts the VAT from each amount instead of adding it.
| Difference looks like… | Most likely cause |
|---|---|
| A round, fairly large amount | Reserve not posted (1) |
| About 20% of your standard-rated sales | Tax added on top (8) |
| A few percent, on a euro or dollar settlement | Currency conversion (3) |
| Exactly the settlement total | Duplicate invoice (7) |
| Equal to the VAT on cross-border orders | MF VAT withholding missing (6) |
| Small and odd | Rare lines missing (5) |
Every cause above comes from posting a settlement partly or twice. TrueBooks reads the whole settlement report, posts every line — reserves, withholdings and reimbursements included — in the settlement's own currency, and blocks a second invoice for the same settlement. Its integrity check compares each posted invoice with Xero and flags any that no longer match. See how the Amazon Xero integration works or start a 30-day free trial.
Yes. If every line of the settlement has been posted — including reserves and currency conversion — the invoice total equals the amount Amazon paid into your bank, to the penny. Any difference means something in the settlement hasn't been posted, has been posted twice, or belongs to a different settlement.
Usually because Amazon has held back a reserve. The settlement report shows the amount held as a Current Reserve Amount line and the amount released from last time as a Previous Reserve Amount Balance line. Both have to be posted, or the invoice will be higher than the deposit.
Only as a last resort. A suspense entry hides the real cause, and if the missing amount was a fee or a VAT line your profit and VAT return will be wrong. Find the cause first; the checklist on this page covers almost every case.
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