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How to allocate a credit note in QuickBooks

QuickBooks Online allocates a credit note, which it calls an adjustment note, in one of two ways. With the Automatically apply credits setting on, the note goes against the customer's oldest open invoice for you; with it off, you apply it by hand in Receive payment.

  • By Book Keeping Pros
  • Sources checked 17 Oct 2026
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Key takeaways

  • With Automatically apply credits turned on, QuickBooks puts an adjustment note against the customer's oldest open invoice and carries any remainder to the next oldest.
  • Intuit notes that the Automatically apply credits setting only affects the next invoice created, so any note it hasn't applied goes on by hand in Receive payment.
  • Until a note is linked to an invoice, both keep open balances on the Customer Balance Detail report.

Before you start

The adjustment note has to exist before it can be allocated. If it isn't saved yet, create it first with the how-to on creating a credit note, then come back here.

Decide whether QuickBooks should do the allocating. With the setting on, it applies notes to the customer's oldest open invoices without being asked. Intuit suggests turning it off if you raise a lot of invoices and adjustment notes for customers, or if particular notes have to go against particular invoices.

Bear in mind Intuit's note that the setting only affects the next invoice created, not existing invoices in Receive payment. Any note the setting hasn't applied goes on by hand, with the steps below.

Steps

  1. Select + New (or + Create), then choose Receive payment.
  2. From the Customer dropdown, pick the customer. When they have credits, the form includes a Credits section.
  3. In the Outstanding Transactions section, select the open invoice the note should reduce.
  4. In the Credits section, select the adjustment note, or the notes, you're applying.
  5. In the Payment column against that invoice, enter how much of the credit to put towards it.
  6. Leave the Payment method, Reference no, Deposit to and Amount received fields blank.
  7. Complete the rest of the form, including the Payment date.
  8. Check the total is right with the note applied, then select Save and close.

Note

To let QuickBooks allocate notes for you, go to Settings and select Account and settings. Open the Advanced tab, select Edit in the Automation section, and turn on the Automatically apply credits switch. Select Save, then Done. Switch it off again if you'd rather pick the invoice yourself each time.

What changes afterwards

When QuickBooks allocates a note automatically, the outcome depends on the amounts. A note equal to the invoice leaves both showing as Closed. A smaller note shows as Closed and leaves the invoice Partial. A larger note clears the oldest open invoice and moves on to the next oldest, and if no open invoices remain, the note's status shows as Unapplied.

With the setting off, a note you haven't linked stays open alongside the invoice. The Customer Balance Detail report shows open balances on both, and they appear as Open on the Customer and Sales transaction pages until you apply the note. Afterwards, the Customer Balance Summary report, under Reports and Standard reports, shows the customer's open balance in its Total column.

An automatic allocation that landed on the wrong invoice can be taken off. Open that invoice and select the blue link for the credit applied, which opens the payment transaction. Select More, then Delete, and select Delete again to confirm. That removes the payment transaction linking the credit to the invoice.

If it doesn't work

No Credits section in Receive payment? It only appears for a customer who has credits. Turned the setting on, yet an existing invoice still shows the full amount owing? The setting doesn't reach invoices already in Receive payment, so apply the note to that one by hand.

General information

This how-to follows Intuit's own help for QuickBooks Online. Screens change between versions, so if yours looks different, use the Intuit article in the sources. It is general information about using the software, not advice about your business. Sources checked 17 October 2026.

Sources

  1. Handle customer adjustment notes and delayed credits, QuickBooks Online help (Australia)

    Intuit Australia Pty Ltd. Current at 17 October 2026, released 17 October 2026. Checked 17 October 2026.

    QuickBooks is a trademark of Intuit Inc. Licence: Intuit Australia legal terms (facts quoted with attribution, no endorsement implied).

  2. Record invoice payments, QuickBooks Online help (Australia)

    Intuit Australia Pty Ltd. Current at 17 October 2026, released 17 October 2026. Checked 17 October 2026.

    QuickBooks is a trademark of Intuit Inc. Licence: Intuit Australia legal terms (facts quoted with attribution, no endorsement implied).

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