How Do I Process a Client Payment?

Once a Client Invoice is sent out, it reflects a Sent status. It stays in this status until one of two things happens:

  • A payment covering the full balance is entered into Discovery as a Client Payment. The invoice then changes to Paid.
  • The payment due date passes, and Discovery automatically changes the status to Delinquent.

A Client Invoice with a status of Sent or Delinquent can accept a Client Payment. Once you receive a payment, you'll record it in Discovery as a Client Payment.

Before Client Payments can be processed, you need at least one Receipt Location, and each Receipt Location needs a GL account from your accounting integration. Your Accounts Receivable GL Account should also be set. Please see either QuickBooks Online Integration or QuickBooks Desktop Integration on how to complete this step.

Note: If Sync Client Invoices with QuickBooks is turned on, record client payments in QuickBooks Online, not Discovery. Payments recorded in QuickBooks update the invoice's balance and status in Discovery automatically. A payment entered only in Discovery isn't sent to QuickBooks, and the invoice's balance can be overwritten the next time it syncs from QuickBooks.

Discovery can handle a variety of Client Payment scenarios. The most straightforward is one payment (e.g. a single check) for one Client Invoice. In this example, Pizza House sent check #1357 for $250.00 to pay invoice #77. Here's how to process it:

One Client Payment | One Client Invoice

1
Click on Revenue in the left-hand navigation. This opens the Invoices tab.
2
Click on the Payments tab.Revenue in the navigation and the Payments tab
3
Here, you'll find all Client Payments that have been processed in Discovery. To process new payments, click the New Batch button.The New Batch button on the Payments tab
4
Select a Payment Method. This article uses Check; the columns in the payment table change to match the method you choose.Payment Method set to Check
5
Select a Receipt Location.The Receipt Location list
Note: Receipt Locations need to be set up in advance to appear here. Please see the How Do I Set Up Receipt Locations documentation on how to do this.
Once both are selected, the payment table appears below.
6
Provide a Receipt Date. It defaults to today.The Receipt Date field
7
Discovery fills in a Batch Name for you. Change it if you prefer; each batch name must be unique.The Batch Name field Now you can fill in the payment table. Each row applies a payment to one invoice.
8
Provide the Check Number.Check Number entered in the payment table
9
Provide the Check Amount.Check Amount entered in the payment table
10
Provide the Check Date.Check Date entered in the payment table
11
Provide the Remitter Name.Remitter Name entered in the payment table
Tip: If the remitter name matches one used on an earlier payment, the invoice list in the next step only shows that company's invoices.
12
Double-click the Invoice Number cell. This opens a list of Client Invoices that are Sent or Delinquent, each showing its amount due. Select your invoice from this list.The invoice list open in the Invoice Number cell

Selecting an invoice fills in the Client Company and Client Account cells for you.
13
Enter an Applied Amount.Applied Amount entered in the payment table

Note: The Applied Amounts for a check must add up exactly to the Check Amount. When one check pays one invoice, the two amounts must match. If you receive a processing error, make sure these amounts match.

You can partially pay a Client Invoice, as long as the whole check is applied and the amount is less than the invoice's balance (e.g. Client Invoice Balance = $700, Check Amount = $500, Applied Amount = $500, new Client Invoice Balance after payment = $200).

14
Repeat for any other Client Payments you want to process in this batch.
15
When you're finished, click the Apply Payments button.The Apply Payments button
16
The Client Payment now appears on the Payments tab in Revenue. To view a Client Payment's details, click its row.A Client Payment row on the Payments tab

Another common scenario is one payment (e.g. a single check) for multiple Client Invoices.

In this example, Office Co. sent check #9753 for $1,780.00. It pays the amount due on these three Client Invoices exactly:

  • #111 | $780.00
  • #112 | $725.00
  • #118 | $275.00

Here's how to process this type of Client Payment:

One Client Payment | Multiple Client Invoices

1
Click on Revenue in the left-hand navigation. This opens the Invoices tab.
2
Click on the Payments tab.Revenue in the navigation and the Payments tab
3
Here, you'll find all Client Payments that have been processed in Discovery. To process new payments, click the New Batch button.The New Batch button on the Payments tab
4
Select a Payment Method.Payment Method set to Check
5
Select a Receipt Location.The Receipt Location list
Note: Receipt Locations need to be set up in advance to appear here. Please see the How Do I Set Up Receipt Locations documentation on how to do this.
Once both are selected, the payment table appears below.
6
Provide a Receipt Date. It defaults to today.The Receipt Date field
7
Discovery fills in a Batch Name for you. Change it if you prefer; each batch name must be unique.The Batch Name field Now you can fill in the payment table, using one row for each invoice the check pays.
8
Provide the same Check Number on all three rows.The same Check Number on three rows
9
Provide the same Check Amount on all three rows. This is the full amount of the check, not the amount for each invoice.The same Check Amount on three rows
10
Provide the same Check Date on all three rows.The same Check Date on three rows
11
Provide the same Remitter Name on all three rows.The same Remitter Name on three rows
Discovery treats rows with the same Check Number, Check Amount, Check Date and Remitter Name as one payment.
12
Double-click the Invoice Number cell on the first row. This opens a list of Client Invoices that are Sent or Delinquent, each showing its amount due. Select your first invoice from this list.The invoice list open in the first row's Invoice Number cell Selecting an invoice fills in the Client Company and Client Account cells for you.
13
Repeat for the remaining two invoices.Three invoice numbers selected
14
Enter an Applied Amount for each Client Invoice.An Applied Amount on each of the three rows

Note: When one check pays multiple Client Invoices, the Applied Amounts must add up exactly to the Check Amount, and every row for that check must have the same Client Company. If you receive a processing error, check these first.

15
Repeat for any other Client Payments you want to process in this batch.
By default, the payment table loads with 25 rows. If you need more, place the cursor in any cell of the last row and press the Return/Enter key on your keyboard once for each row you need to add.
16
When you're finished, click the Apply Payments button.The Apply Payments button

What Happens in Your Accounting System

When you click Apply Payments, Discovery creates one journal entry for the batch:

  • Numbered PMT-0000001, PMT-0000002, and so on.
  • Dated the batch's Receipt Date.
  • A debit to the Receipt Location's GL Account and a credit to your Accounts Receivable GL Account, each for the batch's total.

Like other journal entries, these aren't sent to QuickBooks automatically:

  • QuickBooks Online: go to Settings → Quickbooks Online and click Send Unposted Entries To Accounting System.
  • QuickBooks Desktop: go to Settings → Quickbooks Desktop → Journal Entries, click Create New Export, then download the file from the Exports (iif) tab and import it into QuickBooks.

Example (QuickBooks Online)

A client payment batch for one credit card payment

A payment batch dated 10/21/2026: one $1,040.00 credit card payment, recorded to the Globo Payment Processing receipt location and applied in full to invoice 122079.

The journal entry Discovery created for the payment batch

When you click Apply Payments, Discovery creates journal entry PMT-0000002, dated the batch's Receipt Date. It debits $1,040.00 to the Receipt Location's GL Account (Undeposited Funds) and credits $1,040.00 to your Accounts Receivable GL Account (Discovery Receivables).

The same journal entry in QuickBooks Online

The same journal entry in QuickBooks Online after Send Unposted Entries To Accounting System: same number, date, accounts and amounts. The Accounts Receivable line's description is "Accounts Receivable", and the other line's is "Payments for" plus the receipt date.

This payment pays the example invoice from How Do I Send a Client Invoice? That invoice's journal entry debited $1,040.00 to Accounts Receivable. This entry credits the same $1,040.00, which clears it.

Voiding and Refunding Client Payments

After a payment has been recorded, you may need to reverse it entirely. Discovery supports two ways to do this: voiding a payment and refunding a payment.

Follow this link to learn how to void or refund a payment.

What to Do When a Client Overpays Their Invoice

If a payment is larger than the invoice it's paying, don't apply the full amount to the invoice — a sent invoice can never have a negative balance. Instead, apply the invoice's amount due to the invoice and the remainder to the client's account, where it's held as an unapplied credit until it can be applied to a future invoice or refunded. For the full walkthrough, including how to move the credit onto the customer's next bill and how to keep track of outstanding credits, see Handling Customer Overpayments.

If you have additional questions or need more in depth information, please feel free to send us a message using the help beacon in the lower right-hand corner.

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