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Partial payment: what to do when a customer pays part of an invoice

By The AR Agent team · · 7 min read

A partial payment is when a customer pays some, but not all, of an invoice. The first job is to find out why the amount is short, then record what arrived against the invoice so the open balance is right, and ask for the remainder by a specific date.

Most short payments have an ordinary cause. Treat it as a question to answer, not a fight to start.

Why do customers make a partial payment?

Short payments fall into a few groups. Knowing which one you have decides your next step.

  • A deduction. The customer took off a discount, a fee, a retention amount or a charge they believe you owe them. Sometimes it is right. Sometimes it is an early payment discount they did not earn.
  • A dispute on one line. They accept most of the invoice but question one item, so they pay the rest and hold that line.
  • Cash flow. They pay what they can now and the rest later. This is the case most likely to drag on.
  • A process issue or error. The payment was matched to the wrong invoice, an old amount was paid, or a bank fee came off a wire transfer.

What should you do first?

Do not send a standard reminder for the balance yet. Find out which of the cases above you are dealing with.

  1. Check the remittance advice. It should list which invoices a payment covers and any deductions. If none arrived, ask for it. See our guide to remittance advice.
  2. Compare it with the invoice. Is the gap a round number, a percentage, or a single line?
  3. Check your own records. Did you agree a discount, issue a credit memo, or send a revised quote?
  4. Ask a short, specific question. "We received $3,000 against invoice 1042 for $4,200. Could you tell us what the $1,200 difference relates to?"

If the answer is a dispute, handle it as one. Our guide to invoice disputes covers how to resolve a query on one line without holding up the rest.

How do you record a partial payment?

Record the money against the original invoice, not as a separate unapplied receipt. QuickBooks and Xero both let you enter a payment for less than the invoice total, and the invoice then shows as partly paid with the remaining balance still open.

Say a design studio invoices $4,200 and receives $3,000. The invoice stays open with $1,200 due. The original due date still applies to that balance unless you agree a new one.

A few rules keep the books clean:

  • Do not write off the difference straight away. Reduce the invoice only once you accept the deduction, using a credit memo so the reason is on record.
  • Do not raise a new invoice for the balance. It breaks the link to the original.
  • Keep the aging honest. The balance ages from the original due date, as your accounts receivable aging report should show.
  • Note the reason, so whoever follows up next knows the history.

Does accepting a partial payment waive the rest?

Usually not. In most ordinary cases, banking part of what you are owed does not cancel your right to the remainder. There is one important exception in the US, and it catches people out.

This is general information about US law, not legal advice. Talk to a lawyer about a specific case.

"Payment in full" checks and accord and satisfaction

Under section 3-311 of the Uniform Commercial Code, a claim can be discharged when a customer pays with a check or other instrument and all of the following apply:

  • The customer tendered it in good faith as full satisfaction of the claim.
  • The amount owed was unliquidated or subject to a bona fide dispute.
  • The check, or a written note sent with it, contains a conspicuous statement that it was tendered in full satisfaction.
  • You obtained payment of it, for example by depositing it.

So a check for less than the invoice, marked "paid in full" and sent while the amount is genuinely in dispute, can settle the whole debt once you cash it.

There are exceptions. A claimant can generally avoid the discharge by repaying the check amount within 90 days, and an organization can protect itself with a conspicuous written notice saying where disputed-debt payments must be sent, if the check went elsewhere. Neither helps if you, or the person responsible for the debt, knew the check was offered in full satisfaction before you collected it.

The UCC applies as each state enacts it, and the wording and case law can differ by state. If a short check arrives with "payment in full" wording on a disputed invoice, pause before depositing it and get advice.

Partial payments with no conditions

A transfer for part of the balance, with no full-settlement wording and no dispute, is normally just a payment on account. Record it, thank the customer, and ask for the rest.

Template: acknowledging a partial payment and asking for the balance

Use this once you know why the payment was short, or when the customer has said they will pay the rest later.

Subject: Payment received for invoice [Invoice number], balance of [Balance]

Hi [Customer name],

Thank you for your payment of [Amount received] on [Payment date] against invoice [Invoice number].

The invoice total was [Invoice amount], so a balance of [Balance] remains open.

Could you confirm that the balance will be paid by [Requested date]?

If any part of the invoice is being queried, let me know which line and I will look into it straight away.

Thanks,

[Your name]

If the balance stays unpaid, our past due invoice email templates cover the later stages.

When should a partial payment become a payment plan?

One short payment is a conversation. A pattern of short payments is a plan nobody agreed.

Consider a written plan when:

  • The customer says they cannot pay the balance in one go.
  • They have paid odd amounts two or three times with no clear end date.
  • The balance is large compared with your monthly revenue.

Our payment plan agreement guide includes a template. Until a plan is agreed, keep asking for the full balance by a date.

Frequently asked questions

Should I refuse a partial payment?

Usually there is no reason to. Money on account reduces your risk, and in most cases accepting it does not waive the rest. The exception in the US is a check marked as full payment on a disputed amount, which can settle the claim under UCC 3-311 once you cash it. If you see that wording, pause and get advice first.

How do I show a partial payment on an invoice?

Record the payment against the original invoice in your accounting software. The invoice then shows the amount paid and the balance due, and so does any statement of account you send.

Can I charge a late fee on the unpaid balance?

Only if your agreed terms allow it and it is lawful where you trade. In the US, rules on late fees and interest vary by state and by contract. Our guide to late fees on invoices covers what to check before applying one.

What if the customer never explains the short payment?

Ask once more, specifically, with the invoice number, the amount received and the difference. If there is still no answer, follow up on the balance as an overdue amount through your normal sequence, and keep a note of each request.

How The AR Agent handles this

The AR Agent follows up overdue balances by email, using the invoices and payments already in QuickBooks or Xero. When a customer replies to explain a short payment, it reads the reply and works out what is behind it. If the gap is a query on one line, it pauses normal chasing and brings the dispute to the right person. If the customer says the balance will follow on a date, that becomes a tracked payment promise, and it follows up if the date passes. When the reply needs judgement, such as a proposed deduction, it asks your team. Every email and promise is kept on the customer's record.

Talk to us: our AI agent chases your invoices until you are paid.

Sources

  • UCC 3-311 accord and satisfaction: good faith tender as full satisfaction, unliquidated or bona fide dispute, conspicuous statement, obtaining payment, the organization notice and 90-day repayment exceptions, and the knowledge rule -> https://www.law.cornell.edu/ucc/3/3-311

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