How to mark invoices as paid in bulk in Xero

Sometimes hundreds of invoices or bills in Xero show as unpaid when the money was settled long ago: after a move from another system, when payments were recorded somewhere else, or after a write-off was agreed with your accountant. Xero has no button to mark a whole list as paid. This guide shows how to do it from an Excel or CSV list with Paysweep, checked against Xero first, and how to keep it reversible.

Last checked 25 Oct 2026 against Xero’s published API description.

Why this comes up

An old system was switched off and its open invoices came over to Xero, but the payments did not. A customer paid through a platform that settles in one lump sum. A team recorded receipts in a spreadsheet for a year. In each case the aged receivables or payables report is full of documents that are not really open, and each one needs a payment to close it.

The by-hand way

Open each invoice, record a payment for the amount due to the agreed account, and save. With a few dozen this is an afternoon. With several thousand it is not realistic, and it is easy to pay one twice or miss one.

Cleanup mode: choose open documents without a file

On the Pay tab, turn on Cleanup mode. Choose invoices, bills or both, then filter by contact name contains, due date before a day, currency or maximum amount due. Press Find open invoices. The list contains approved documents with an amount still due, in pages of up to 100 rows.

Tick the documents you want to clear. Previous page and Next page keep your selection; a successful new search clears it. Choose one payment account and one payment date, then press Preview. The account list contains active bank accounts and accounts enabled to accept payments in Xero, shown by code. It does not create a clearing account for you.

Preview reads the selected documents again and plans each full current amount due. Review the totals and any rows to fix, then type PAY and the ready payment count to record them. Cleanup mode uses the same result CSV and 30-day Undo button as a file run. You can select at most 2,500 documents per run; an oversized request is refused without cutting off rows. If you need different amounts, references or currency rates per row, use a file instead.

Preparing the list

Paysweep needs one row per invoice or bill with its number (or its Xero InvoiceID) and a payment date. The amount can stay blank: a blank amount pays exactly what is due. The account can come from one default on the page, so the file can be as simple as:

Invoice Number,Payment Date
INV-0102,2026-09-30
INV-0117,2026-09-30
BILL-2210,2026-09-30

Excel files are read in your browser from the first sheet; date cells are read as dates. Blank rows are skipped and row numbers still match your sheet.

What is checked

• The number matches exactly one invoice or bill in the organisation.
• It is approved and has something due. Drafts, voided and already paid documents are rows to fix.
• The account exists, is active and accepts payments, and its currency fits.
• The payment date is after the organisation’s lock date.
• Right before each payment the invoice is read again; if its amount due changed since the preview, that row is skipped.

A worked example

Say your business moved to Xero last year and brought 1,800 customer invoices across from the old system as open, while the money for most of them had already come in before the move. Your accountant agrees that 1,650 of them were settled and should be cleared against a clearing account, and gives you the list.

You paste the 1,650 invoice numbers into a sheet with one payment date, upload it, and set the clearing account code as the default. The preview shows 1,641 payments ready and 9 rows to fix: 6 invoices that someone already paid by hand last month (nothing is due), 2 numbers that are not in Xero, and 1 invoice still in draft. You download those 9 rows for your accountant and run the 1,641. The run spreads over the organisation’s daily Xero budget and finishes on its own; the result CSV is the record of what was cleared.

Things to agree before you run it

• The date. The payment date decides the period the payment falls in. A date in a closed period is refused by the lock date check, so agree a date that is open.
• The account. A clearing account keeps these entries apart from your real bank accounts, which makes them easy to find and review later.
• The list. Paying in full means the whole amount due on each document. If some were paid in part, put the part amount on those rows instead of leaving it blank.
• The way back. Agree that any run can be undone within 30 days, so a wrong list or a wrong date is fixed by undoing the run and recording it again, not by editing payments one at a time.

Doing it with Paysweep

1. Agree the account first. Decide with your accountant which account the clearing payments go to, for example a clearing account set to accept payments, or the bank account the money really went into.
2. Export the list. From your Xero invoice or bill list, or from your old system, make a sheet with one invoice number per row. Leave the amount column out or blank.
3. Upload it. Connect your organisation, choose the file, check that the payment date column is matched, and set the default account code.
4. Read the preview. Every row pays the full amount due. Invoices that are not approved, already paid, or dated before your lock date are listed as rows to fix.
5. Confirm. Type PAY and the number of payments.
6. Keep the result CSV. It lists every row with its outcome and the Xero IDs, for your records and for your accountant.

What to expect

Every payment is its own call to Xero with a fixed idempotency key, read back after it lands. A run pauses when the organisation’s daily Xero budget is used and continues the next day by itself, so a very large clean-up may take more than one day.

The first 3 payments in each organisation are free. A one-off clean-up usually fits the $39 pass (7 days, up to 300 payments); $19 a month per organisation has no limit; both prices are excl. VAT/sales tax. See pricing, and the CSV guide for every column Paysweep reads.

Questions

Related guides

• How to bulk record payments in Xero from a CSV file
  What Xero offers for many payments, the by-hand way, the CSV layout, and doing it with Paysweep.
• How to undo bulk payments in Xero
  Removing payments by hand, and how Paysweep undo works within 30 days and what it leaves alone.
• Pricing
  Free previews, a $39 pass or $19 a month, excl. VAT/sales tax.
• Paysweep overview
  What Paysweep does with your file, the checks on every step, and how undo works.