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Applying a Payment to an Invoice with Bank Fees

Learn how to reconcile payments that are slightly less than the invoice amount due to bank fees.

Kolleno Support avatar
Written by Kolleno Support
Updated over 2 weeks ago

Sometimes a customer’s payment is slightly less than the invoice amount because of bank fees or transfer charges. In this case, you can still match the payment to the invoice by recording the fee adjustment during reconciliation.

For a step-by-step demonstration, watch our short video guide:


Step 1: Select the payment

  • Open your Bank Transactions list.

  • Choose the payment you want to apply either by manually finding it or selecting from suggested matches.


Step 2: Review the balance check section for the difference amount

  • If the payment amount is lower than the invoice balance because of bank fees, the system highlights the difference.

  • In this example, you received a payment of 100 for an invoice of 108.25. You’ll need to create an adjustment for 8.25.


Step 3: Record the bank fee adjustment

  • In the adjustment field, enter the fee amount.

  • The adjustment ensures that Total of matched items equals the Invoice unmatched amount.

  • This way, payment + bank fee = full invoice amount.


Step 4: Confirm the balance check

Verify that:

  • The matched payment + bank fee adjustment = invoice unmatched amount.

For the invoice to be fully cleared, the amount applied must equal the invoice unmatched amount.


Step 5: Complete the match

  • Click Match to create the link.

  • A pop-up confirms what will be pushed to NetSuite — the customer payment applied to the invoice, with the fee adjustment recorded separately.

Note: At this point, the match is saved in Kolleno but not yet reconciled to NetSuite. This provides an additional safety check.


Step 6: Reconcile to NetSuite

  • Once confident the match is correct, click Reconcile.

  • Within 1–2 minutes, you will see:

    • The invoice balance reduced to 0, and

    • The applied payment record and adjustment journal entry in the invoice’s history.


You have now successfully applied a payment to an invoice while accounting for bank fees.

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