Xero: one customer payment for many invoices, from the remittance PDF

A customer sends one transfer and a remittance advice PDF that lists the invoices it covers. In Xero you now have to find each invoice and record its payment. This guide shows Xero’s own way to do it by hand, then how Paysweep reads the PDF in your browser, matches the invoice numbers and amounts to your open invoices, and records the payments only after you have looked at a preview and typed the confirmation.

Xero Central steps checked 7 Nov 2026; API details checked 25 Oct 2026.

Xero’s own way, by hand

For one customer payment that covers several sales invoices, Xero has a batch deposit: tick the invoices on the Awaiting Payment list and enter the payment once. Xero Central lists the limits: up to 50 invoices at a time, base currency invoices, and a base currency bank account. If your remittance has fewer than fifty lines and every invoice is in your base currency, this is a good option, and it is free.

Without it, you open each invoice, add the payment with the date, the account and the amount from the remittance, and save. Check the amounts against the PDF yourself, one by one.

What is different about Paysweep

Paysweep records one payment per invoice (through Xero’s API, with the preview and typed confirmation first), not one combined deposit. We have not tested how those payments reconcile against a single bank statement line in Xero, so if you need one combined deposit for matching, use the batch deposit above.

What Paysweep adds is the reading and the checking: it takes the invoice numbers and amounts from the PDF, compares them with what Xero says is open, and shows where they disagree before anything is recorded.

What the PDF has to look like

• Text, not a picture. If you can select and copy the numbers in a PDF viewer, Paysweep can read them.
• One row per invoice, with the invoice number and the amount paid on the same row. Amounts with two decimals, in US (1,250.00) or European (1.250,00) form; negatives in brackets or with a minus sign.
• The invoice number exactly as in Xero.
• A printed total, a payment date and a payment reference are used when they are labelled (for example “Total remitted”, “Payment date”, “Payment reference”). None of them is required.

Doing it with Paysweep

1. Open Paysweep. Read what it asks Xero for, then connect the organisation the invoices belong to.
2. Choose the PDF. It is read in your browser. If it is a scan or locked with a password, Paysweep says so and offers a CSV to fill in.
3. Read each line. Every invoice number on the PDF is looked up in Xero. Lines that match exactly are ticked. Lines that pay less than is due, or do not match, are marked and left for you.
4. Compare the totals. The total printed on the PDF, the sum of its lines and the sum of the ticked lines are shown to the cent, with the difference.
5. Enter the date and the account. The payment date is taken from the PDF when it states one; the bank or clearing account is yours to choose.
6. Continue to the payment check. This is the same preview as for a CSV file. Type PAY and the number of payments to record them.
7. Open the result. Each payment has a link to its invoice in Xero, and you can undo the run for 30 days.

How each line is judged

• Ready. The number exists, the invoice is awaiting payment and the amount on the PDF equals the amount due.
• Pays less than is due. Shown with the amount due. Ticking it records the smaller amount.
• More than is due. Not recordable. Check the invoice or ask the customer.
• Not found, or more than one document has the number. Not recorded.
• A bill, a draft, already paid, nothing due. Not recorded, with the reason.
• Another currency. Not matched here. Use a CSV with the bank account in that currency and the exchange rate.
• Printed twice, or a credit line. Not recorded.

A worked example

A customer’s remittance lists six invoices and prints a total of 9,545.90. In Xero, three of the invoices are awaiting payment for exactly the amount on the PDF. One is awaiting payment for 700.00 while the customer paid 612.40. One is still a draft, and one number is not in Xero at all. Paysweep ticks the three exact lines (6,635.85), marks the short payment and leaves it unticked, and marks the draft and the missing number as not recorded. It also points out that the six lines on that PDF add to 9,535.90, ten less than the total the customer printed. You decide what to do with the short payment, the draft and the missing invoice, and record the three that are certain.

Remittances with a discount column

Some remittances print the invoice value and a discount in separate columns, with no column for the amount actually paid. The invoice value alone would close the invoice for more than arrived. When Paysweep sees a discount column and no paid column, it stops before looking anything up and asks which amount to record: the amount as printed, or the amount minus the discount. Each choice shows what it adds up to against the printed total. Nothing is chosen or ticked for you. If the file has a column for the amount paid, that column is used and no question is asked.

When a remittance has two reference columns, such as Our Ref and Your Ref, Paysweep takes Your Ref as your invoice number and Our Ref as the payer’s own number. In running text, a number that follows the word invoice is preferred over one that follows order or PO.

The totals, to the cent

Three amounts are shown: the total the payer printed, the sum of the lines on the PDF, and the sum of the lines you have ticked. If the ticked lines are not exactly the printed total, the difference is stated, for example when the PDF itself does not add up, or when a line was left out. Fixing the difference is up to you; Paysweep records only what you have ticked.

What is free, what is not

Connecting, reading the PDF and every preview are free, and so are the first 3 payments in each organisation. After that a $39 one-off pass covers one organisation for 7 days and up to 300 payments, and $19 a month per organisation has no limit; both prices are excl. VAT/sales tax. One run records up to 2,500 payments. See pricing. For the CSV route, read importing invoice payments from a CSV.

Questions

Related guides

• Xero import invoice payments: record payments on invoices from a CSV
  Xero’s own batch deposit and Conversion Toolbox, where they stop, and importing invoice payments from a CSV with Paysweep.
• Xero: mark multiple invoices as paid at once
  Xero’s batch deposit and batch payment, their limits, and clearing many open invoices from a list 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.