What's the difference between a remittance advice and a receipt?

A remittance advice comes from the payer and says what they are paying. A receipt comes from you and confirms what you received.

Why record a multi-invoice payment as a single payment?

Because your bank shows a single deposit. One payment applied to several invoices keeps bank reconciliation simple.

What is an unearned discount?

A discount a customer takes after the discount window has passed. It's usually handled as a deduction to accept or dispute.

What is remittance advice? How to match customer payments to invoices

6 min readUpdated September 29, 2026By the thruflow team

The short answer

A remittance advice is the note a customer sends with a payment that lists which invoices it pays, how much against each, and any discounts or deductions taken. You use it to apply one deposit across the right open invoices, record each discount or deduction, and leave nothing unapplied.

What a remittance advice contains

Who paid, the payment date and the total.
How they paid, with a reference: a check number, an ACH trace number or a wire reference.
One line per invoice paid: the invoice number (yours, or sometimes their own reference or your PO number), the invoice amount, any discount taken, any deduction with a reason, and the net amount paid.

The formats it arrives in

A PDF attached to an email from the customer's accounts payable team.
A spreadsheet or CSV exported from the customer's AP system.
The body of a bank or ACH payment notification email.
A download from the customer's supplier portal.
A paper stub that comes with a check.

How to apply one payment across many invoices

Identify who paid, from the remittance or the sender, and list their open invoices.
Match each line to an open invoice: by your invoice number first, then the number your accounting system gave it, then the PO number, and only then by an amount that just one open invoice has.
Check that the lines add up to the amount deposited.
Record any early-payment discount taken within your terms as a discount, so the invoice closes at its full value.
Decide on each deduction: accept it and issue a credit, or dispute it and keep it owed.
Record the whole thing as one payment with a line per invoice, so it matches the single deposit on your bank statement.

Common problems, and what to do

The remittance quotes the customer's own reference, not your invoice number: match by PO number or amount, and confirm.
A discount taken after the window: treat it as a deduction to accept or dispute, not as a discount.
A short payment with no reason: keep the difference open and ask the customer before you write it off.
Several invoices paid under one reference: rely on the amounts on the remittance, not the reference alone.
The money arrives before the remittance: record the deposit, and apply it when you know what it's for.

How thruflow does it

Customers can send remittance advice to your own payments address, as a PDF, an Excel or CSV file, or in the email itself. thruflow reads it, matches each line to an open invoice by number, QuickBooks number, PO or amount, takes early-payment discounts that were earned, and lets you accept or dispute each deduction. It's recorded as one payment, and one payment in QuickBooks.

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Questions

What's the difference between a remittance advice and a receipt?: A remittance advice comes from the payer and says what they are paying. A receipt comes from you and confirms what you received.
Why record a multi-invoice payment as a single payment?: Because your bank shows a single deposit. One payment applied to several invoices keeps bank reconciliation simple.
What is an unearned discount?: A discount a customer takes after the discount window has passed. It's usually handled as a deduction to accept or dispute.