Apply the amount that arrived to the invoice, and it stays open for the rest. If you accept the shortfall, record a credit note for the difference.
Why a short payment waits for you
Streamlined applies a bank transfer or check on its own only when its amount matches an open invoice. A wire that lost bank fees on the way doesn't match, and neither does a payment with a deduction taken off. It waits on the Transactions page under "payments couldn't be matched to an open invoice".
Apply what arrived
Go to Transactions and click Match on the payment.
Find the invoice on the Auto-match or Browse tab and add it.
Click Continue.
Change the invoice's Apply amount to the amount that arrived, so Remaining is zero.
Click Confirm.
The invoice's balance drops by the payment, and the difference stays open.
Write off the difference
If you won't collect the rest, record a credit note for it.
Open the invoice and click More actions (⋯).
Choose Record credit note. The Amount starts at the open balance.
Add a Memo, such as "Bank fees on wire", and click Save.
A credit note that brings the balance to zero doesn't email your customer. See credit notes and debit notes.
Tip: To collect the rest instead, leave the invoice open. Your customer can pay the balance like any other.
A short payment across several invoices
Add every invoice the payment covers. Lower the Apply amount on each one it falls short on, until Remaining is zero. A credit note applies to one invoice, so then record one on each of those invoices. See apply one payment to several invoices.
Who can use this feature?
Team members with Transactions and Invoices access
Available on all plans