When receiving payments through third-party providers, the amount deposited into your account may be lower than the invoice total due to processing fees. COUNT allows you to properly record these transactions so your invoice is marked as fully paid while also capturing the fee as an expense.

This article will guide you through how to handle third-party payment or merchant fees in COUNT.

Benefits of Recording Third-Party Fees Correctly:

• Accurate Income Reporting: Ensure your invoice reflects the full amount paid by your client.
• Proper Expense Tracking: Record processing fees separately for better financial visibility.
• Clean Reconciliation: Keep your books balanced without leaving partial invoice payments.

Recording a Third-Party Payment Fee:

Step 1: Navigate to the Invoices & Estimates page

1. Go to Invoices **& Estimates **and look for the invoice you want to apply the payment to
2. Click Record Payment or Credit, then Select Transaction(s)

3. Choose the payment transaction (e.g., the lower amount due to fees)
4. Apply the transaction to the invoice as a partial payment. Learn more here: Record an Invoice Payment in COUNT

Step 2. Apply the merchant fee to clear the remaining balance

1. In the Invoice listing, locate the invoice and click on Record Payment or Credit **then click **Select Transactions.

2. Click Record a Payment
3. Select Apply Merchant Fee to account for the remaining balance

5. Then click Mark Invoice Paid & Apply Merchant Fee

Step 3. After selecting Mark Invoice Paid & Apply Merchant Fee, COUNT will recognize that the remaining balance was withheld by a third-party payment provider.

The system will automatically:

• Mark the invoice as fully paid
• Record the remaining amount as a merchant fee expense

Updated on: 06/05/2026