Record Payments Against Invoices

When money comes in (a check in the mail, cash on site, a bank transfer), you record it as a payment applied to one or more of the customer’s invoices. This article covers the two ways to record a payment (the quick Record payment button on the list, and the full Record Payment screen), reviewing a payment afterward, printing a receipt, deleting a payment, and how deposits, refunds and disputes show up. Online payments made by customers through the Customer Portal record themselves; there is nothing for you to do.

Before you start

At least one unpaid invoice for the customer (see Create and Manage Invoices).
At least one Payment Method set up (Cash, Check, etc.) — the payment form requires one.
Know the split if one check covers several invoices: you’ll enter an amount per invoice.

Steps

Option A: Quick payment from the list (one invoice, fastest)

Go to Billing > Invoices & Payments. On any Invoice row with a balance, click Record payment in the Actions column.
A Record payment window opens showing the invoice number, customer, and open balance. It pre-fills:
- Payment Date — today.
- Amount — the full open balance (edit for a partial payment).
Choose the Payment Method (required) and optionally a Reference (check number, ACH ref, etc.).
Click Record Payment. You’re taken to the new payment’s summary page.

The window checks the amount before anything is saved: it must be greater than zero, in whole cents, and no more than the open balance (“The payment cannot be more than the open balance of $…”).

Option B: Record Payment screen (split across invoices)

Open the invoice and click Record payment (in the header, or in the Action menu; offered on any invoice that isn’t fully paid). The Record Payment page opens with the customer pre-selected and their open invoices listed. You can also switch customers using the searchable Customer dropdown, type to filter.
Enter the Payment Date (pre-filled with today; required, and it can’t be in the future) and pick the Payment Method (required). Reference Number is optional (up to 225 characters).
In the invoice list, select each invoice this payment covers and type the payment amount for each. The totals and the customer’s balance after this payment update as you type.
Click Record payment.

The screen tells you what is missing before it saves: a customer, the date, the payment method, at least one open invoice, and a positive amount within each selected invoice’s open balance, using at most two decimals.

Review the payment — Payment Summary

After recording you land on the Payment Summary page (“Payment recorded successfully. Review any remaining balance below.”), which is also where the payment number on a Payment row in the list takes you. It shows:

Applied Invoices — each invoice the payment touched, with the original amount and the portion applied (invoice numbers are clickable).
Payment Details — customer (clickable), payment date, reference #, payment type, amount received, and the customer’s remaining balance.
Source — an Online badge for portal/Stripe payments or Manual for ones you keyed in. Online payments with a customer-paid card surcharge show it as “+$X.XX processing fee”.
Memo — if one was recorded.

Print a receipt

On the Payment Summary, click Print Receipt (top right). A print-formatted receipt opens in a new tab — with your company document header, the payment details, and the invoices it was applied to — ready for your browser’s print dialog or “Save as PDF”.

Edit a payment

There is no edit screen for payments. If a payment you keyed in was recorded with the wrong amount, date, method, or against the wrong invoice: delete it and record it again correctly.

Delete a payment

Open the payment (from its row in the list, or via an invoice’s Payment History).
Click Delete (top right) and confirm “Are you sure you want to delete this payment?”.
You’re returned to Invoices & Payments with “Payment was successfully deleted!.” Every invoice the payment touched gets its balance back.

Only payments you keyed in can be deleted here. A payment taken online through Stripe, an estimate deposit, and a refund have no Delete button: “This payment was taken online through Stripe, or is an estimate deposit or a refund, so it can not be deleted here. Refund it in Stripe; the refund is recorded here automatically.”

Deposits and credit on account

A deposit the customer paid when accepting an estimate is credit on account until you use it. The customer’s page shows it beside their outstanding balance (it is never subtracted from it), and the customer sees it in the portal too.

Apply it: open the customer’s invoice and click Apply to this invoice on the Customer deposit on file card. The amount is capped at the invoice’s open balance.
Unapply it: if you applied it to the wrong invoice, click Unapply on the deposit’s row in that invoice’s Payment History and confirm. The money goes back to credit on account and the invoice owes it again. If the deposit had closed the job, the job goes back to Invoiced. A refunded deposit can’t be unapplied.

Refunds and disputes (online payments)

Refunds and disputes are handled in your Stripe Dashboard, and the app records the result on its own:

A refund shows as a Refund row in the list, and the invoice owes that amount again.
A dispute (a card chargeback, or a bank payment the bank takes back) is posted to your activity feed as Payment disputed, with the date to respond by. When Stripe takes the money, the payment comes off the books and the invoice shows it as owed again. If you win, the money comes back and the invoice is paid again; if you lose, it stays open. See the portal troubleshooting guide.

What happens next

Recording a payment updates each touched invoice’s status immediately: Partial if a balance remains, Paid when fully covered.
When an invoice is paid in full, its linked job is moved to Closed only if the job’s work is done (Completed or Invoiced) and no other invoice on the job still owes money.
Payments appear as their own Payment rows in the list (with a Manual or Online source badge), and in the invoice’s Payment History table.
Deleting a payment reopens the affected invoices’ balances, and statuses fall back to Partial/Open/Overdue accordingly. If that payment had closed the job, the job goes back to Invoiced.
Payments you record or delete are kept in an audit trail with who did it and when. Contact support if you need that history.

Tips & best practices

Use the list’s Record payment button for the everyday case (one check, one invoice) and the Record Payment screen when a single check covers multiple invoices.
Always capture the Reference for checks and bank transfers — it’s what you’ll search for when the customer asks “did you get my check?”
Don’t try to “fix” an online payment: portal/Stripe payments arrived on their own and reconcile against your Stripe payouts; refund them in Stripe. The Online/Manual totals at the top of the page keep the two streams separate.
Overpayments: the forms won’t let you apply more than an invoice’s open balance, which keeps statuses clean. If a customer genuinely overpays, apply up to the balance and handle the remainder as a credit conversation.

Troubleshooting

No Record payment button on a row: it only appears on Invoice rows with a balance greater than zero. Paid invoices and Payment rows don’t have it.
“Select at least one open invoice.”: on the Record Payment screen you must select each invoice you’re applying money to, not just type amounts.
“Payment for invoice … exceeds the open balance.”: reduce the amount for that invoice; apply any excess to another open invoice.
“Payment amounts can have at most two decimals.”: enter dollars and cents only.
“Payment date cannot be in the future.”: record the payment on the day it arrived, or today.
“Invoice [number] is already fully paid” — someone (or a portal payment) beat you to it; refresh and re-check the balances.
No Delete button on a payment: it was taken online, is an estimate deposit, or is a refund. Refund it in Stripe instead.
“The deposit could not be unapplied. It may already be unapplied, or it was refunded.”: refresh the invoice; the deposit has already gone back, or Stripe refunded it.
Recorded it wrong — delete the payment and re-record; there’s no edit.
A payment I don’t recognize with an Online badge — that’s a customer paying through the Customer Portal via Stripe. See the Customer Portal overview.

Create and Manage Invoices — the invoices these payments apply to
Invoicing Overview — statuses and how payments fit the bigger picture
Deposits on Estimate Acceptance: where deposits on file come from
Batch Billing — generating the invoices in bulk
Automatic Invoicing — hands-off invoice creation
Customer Portal overview — online payments, surcharges, and Stripe setup