Duplicate Amazon Invoices in Xero: Why They Happen and How to Clean Them Up

Short answer: a duplicate Amazon invoice in Xero happens when the same settlement is posted twice — usually because two tools were running at once, a settlement was re-posted after a failed cancellation, or someone entered it by hand as well. Find duplicates by searching Xero for each settlement ID, keep the invoice that matches the bank deposit, and void the other.

Why it matters

A duplicate doubles that settlement's sales, fees and VAT. Your profit is overstated, Box 1 and Box 4 are wrong, and your debtors show money Amazon will never pay. Because only one invoice can be matched to the deposit, the other sits as an unpaid invoice indefinitely.

How duplicates happen

Two tools at once. When switching between connectors, both run for a period and each posts the same settlements. They use different reference formats, so neither spots the other's invoice.
Re-posting after a failed void. A settlement is corrected by voiding and re-posting, but the void fails quietly and the new invoice is created anyway.
Manual plus automatic. Someone keys in a settlement while an integration also posts it.
Whole and split. A cross-month settlement is posted once as a whole and again in two monthly parts.

How to find every duplicate

In Xero, open Business → Invoices and filter to the Amazon contacts (e.g. "Amazon.co.uk").
Search by each settlement ID. Every settlement should appear once.
Look for pairs of invoices with the same total and similar dates — often the giveaway when two tools used different references.
Check old unpaid Amazon invoices. A duplicate is usually the one that never got paid.

How to clean up safely

Pick the keeper: the invoice whose total equals the deposit and is already reconciled.
Free the extra: if the duplicate has a payment or bank match, remove it first.
Void, don't delete: void the duplicate so there's a record of the change.
Check filed VAT periods: if the duplicate was in a submitted return, correct it on the next return or disclose it, depending on size (see the FAQ below).
Stop the cause: turn off whichever tool or process created the second copy.

Switching tools without creating duplicates

The safest switch sets a clear cutover date: the old tool owns every settlement up to it, the new tool owns everything after. TrueBooks' migration does this. It recognises settlements Link My Books already posted to Xero automatically, and for other tools such as A2X you set the date you stopped using them. Either way, nothing before the cutover is posted again.

How TrueBooks prevents duplicates

Every TrueBooks invoice carries the settlement ID in its reference. Before posting, TrueBooks searches Xero for that reference; if an invoice already exists it is voided and replaced rather than duplicated, and the original invoice number is reused. A one-click duplicate scan finds and voids extras across your whole Xero history. See the Amazon Xero integration.

Frequently asked questions

Should I delete or void a duplicate Amazon invoice in Xero?

Void it. Authorised invoices in Xero can't be deleted, and voiding keeps an audit trail showing the invoice existed and was cancelled. If a payment is attached, remove the payment (or unreconcile the bank line) first, then void.

The duplicate was included in a VAT return I've already filed. What now?

Voiding it changes a period you've already reported. HMRC lets you correct errors on your next return if the net value is £10,000 or less, or up to 1% of your Box 6 turnover (capped at £50,000). Larger errors must be disclosed separately. Your accountant can confirm which applies.

Which of the two invoices should I keep?

Keep the one whose total matches the bank deposit and whose lines are correct. If both are identical, keep the one that's already reconciled against the deposit, so you don't have to redo the bank match.

Duplicate Amazon Invoices in Xero