Should we write off small short payments?

Below a limit you set, usually yes: a few dollars of bank fees aren't worth a conversation. Set a small-balance limit and write off only under it, so larger differences are always looked at.

How soon should we follow up a short payment?

Within a week or two of the payment, once the invoice is past due. The longer it waits, the harder it is for either side to remember why.

Is a short payment the same as a partial payment?

A partial payment is often agreed in advance, with more to follow. A short payment is when the customer appears to think they've paid in full.

Short payments: why customers pay less than the invoice, and how to collect the rest

6 min readUpdated October 14, 2026By the thruflow team

The short answer

A short payment is a payment for less than the invoice, where no credit memo, discount or agreement covers the difference. Record what was received, keep the rest open, and find out why: it may be a deduction the customer believes is agreed, an early-payment discount taken late, a bank fee, a dispute about the goods, or a mistake. Then either accept the difference as a credit, on purpose and with a reason, or ask the customer for the rest, naming the invoice and the exact amount.

The usual reasons

A deduction the customer took: damaged or missing goods, a pricing difference, a promotion or allowance, a retailer chargeback.
An early-payment discount taken after its window had closed.
Bank fees taken off a wire or an international payment on the way.
A dispute about part of the order that nobody has told you about yet.
A mistake: the wrong invoice paid, a typo in the amount, or an old price.

Short payment, deduction or discount?

	What it is	What to do
Earned discount	Taken within the discount window on your terms	Record it as a discount; the invoice closes
Deduction	Taken with a reason the customer gives	Accept it as a credit, or dispute it and keep it owed
Short payment	Less than the invoice, with no reason given	Keep it open, find out why, then accept or ask

How to handle one

Record the payment for the amount actually received, against the invoice it pays. Don't close the invoice.
Check the customer's remittance advice and any email for a reason.
Check whether a credit, a return or money on their account already covers the difference.
If there's a reason you accept, issue a credit memo with that reason, so the invoice closes on purpose.
If there isn't, write to the customer within a week or two, while they still remember the payment.
Keep the conversation with the invoice, so whoever looks next knows where it stands.

What to write

Short, specific and polite. For example: "Thank you for your payment of $3,712.50 on October 1 for invoice INV-2041 ($4,125.00). $412.50 is still open on it. If you held it back for a reason, please reply with the details and we'll sort it out. Otherwise, could you send the remaining $412.50?"

Thank them for what they paid, with the date and amount.
Name the invoice and its total.
State exactly what's still open.
Ask for the reason or the rest, and make replying easy.

Keeping it from happening

Put your PO number, terms and any discount deadline on every invoice.
Check prices on each order against the customer's agreed price list before you invoice.
Send statements, so customers see what's still open on their account.
Agree in advance how bank fees on wires are handled.

How thruflow does it

thruflow records part payments as they arrive and keeps the rest open. Recover flags an invoice that's past due and part paid, with nothing for 7 days, and drafts the email above from the facts, answering the customer's own words if they've replied. Credits, returns and deductions are recorded with their reasons, and a small leftover under your limit can be written off.

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Questions

Should we write off small short payments?: Below a limit you set, usually yes: a few dollars of bank fees aren't worth a conversation. Set a small-balance limit and write off only under it, so larger differences are always looked at.
How soon should we follow up a short payment?: Within a week or two of the payment, once the invoice is past due. The longer it waits, the harder it is for either side to remember why.
Is a short payment the same as a partial payment?: A partial payment is often agreed in advance, with more to follow. A short payment is when the customer appears to think they've paid in full.