The quick answer
In NetSuite 2026.2, record the surcharge as a payment adjustment on the customer payment. First give it a reason: go to Setup > Accounting > Accounting Lists, click New with the Type filter set to Payment Adjustment, and create a Revenue reason such as Card Surcharge with an income Account, available on Payment. Then, on the customer payment, apply the invoice, enter the full amount you received in Payment Amount, and add a line on the Payment Adjustments subtab for the surcharge. Unapplied drops to 0.00, the invoice is paid in full, and the payment's GL Impact credits the surcharge to its own account.
The screenshots show sample data. Person and operating-company names are fictional. Use your own records and values when following the steps.
Before you start
This example company adds a 3% surcharge when a customer pays by card. Harbor Lane Veterinary pays invoice INV-4471 for 1,240.00 by card, so 1,277.20 comes in: the invoice plus a 37.20 surcharge. If you apply that payment to the invoice and stop there, the 37.20 sits as an unapplied credit on the customer, even though nobody owes it back.
Payment adjustments are new in NetSuite 2026.2. They put the difference on the payment itself, with its own reason and account, so you don't need a separate journal entry or credit memo to clean it up. A reason can also be made available on customer deposits. In the account used for this example, no feature had to be turned on first, and the Payment Adjustments subtab was already on the payment form.
You need a role that can edit Accounting Lists (the Administrator role can) and one that can create customer payments for this customer. The card was charged outside NetSuite, so this is recording money that already came in. The payment goes to Undeposited Funds, and the invoice and payment share the same subsidiary, currency, and A/R account. Menu paths, reason lists, and account numbers below are the ones in the account used for this example.
Whether you're allowed to charge a card surcharge, and whether it's taxable, depends on card network rules, local law, and your processor agreement. NetSuite only records it.
01. Review the payment adjustment reasons
Go to Setup > Accounting > Accounting Lists and set the Type filter to Payment Adjustment. The list shows the four reasons NetSuite provides: Bank fee, Convenience fee, Overpayment, and Underpayment.
Click Edit next to Underpayment. Type is Expense and can't be changed, and Account is empty but required. In the accounts checked for this guide, none of the four had an account yet, and a reason without an account doesn't show up on payments. Click Cancel. You could give one of these an account, but this example creates its own reason so the name matches what the customer was charged.
02. Create the Card Surcharge reason
Back on Accounting Lists, click New. With the filter on Payment Adjustment, the Payment Adjustment form opens directly. Type Card Surcharge in Name. Choose Revenue in Type, since the surcharge is extra income, and 4620 Card Surcharge Income in Account. Under Available at Transaction Types, click Payment. Click Save.
The saved reason shows Type Revenue, Account 4620 Card Surcharge Income, and Available at Transaction Types Payment.
03. Apply the invoice
Go to Transactions > Customers > Accept Customer Payments and choose Harbor Lane Veterinary in Customer. On the Apply subtab, the Invoices list shows the customer's open invoices. INV-4471, dated 09/08/2026, has Orig. Amt. and Amt. Due of 1,240.00.
Leave Undeposited Funds selected. Check Apply on INV-4471. Its Payment is 1,240.00, and because Payment Amount was still 0.00, NetSuite fills it in as 1,240.00.
04. Enter the amount received
Replace Payment Amount with 1,277.20, the cash that actually came in. In the Summary, To Apply is the payment amount after any adjustments, Applied is what's applied to invoices, and Unapplied is the difference. It now shows To Apply 1,277.20, Applied 1,240.00, and Unapplied 37.20. Saved like this, the payment would leave a 37.20 credit on the customer.
05. Add the payment adjustment
Open the Payment Adjustments subtab. The subtab has Name, Type, Currency, and Amount columns. In Name, choose Card Surcharge. The list only offers active reasons that have an account and are available on payments, which is why Card Surcharge is the only choice here. Type fills in as Revenue and Currency as USD. Type 37.20 in Amount and click Add.
Scroll back up to the Summary. It shows To Apply 1,240.00, Applied 1,240.00, and Unapplied 0.00. A Revenue adjustment takes its amount out of the cash that's left to apply, so the 37.20 is now surcharge income instead of a customer credit.
06. Save and check the GL impact
Click Save. Payment 2318 opens with the status Not Deposited, because the cash went to Undeposited Funds. The Summary shows Applied 1,240.00 and Unapplied 0.00, and the Payment Adjustments subtab keeps the Card Surcharge line.
Open the GL Impact subtab. You can also get there from Actions > GL Impact. The account numbers are this example account's; yours will show your own deposit, A/R, and surcharge accounts.
Check the result
- 1150 Undeposited Funds is debited $1,277.20, the full amount received.
- 1210 Accounts Receivable is credited $1,240.00, the whole invoice, so INV-4471 is paid in full.
- 4620 Card Surcharge Income is credited $37.20 with the memo Card Surcharge.
- The debit equals the two credits: 1,240.00 plus 37.20 is 1,277.20.
The processor-fee case works the other way. If your card processor keeps a fee and deposits less than the invoice total, create an Expense reason that posts to a fee expense account. Enter the net amount deposited as Payment Amount, apply the full invoice, and add the fee as a payment adjustment. The net amount plus the fee equals the invoice, and the GL Impact debits the fee expense account instead of crediting income. If you record the full invoice as the payment and book the processor fee on the bank deposit instead, don't add an adjustment as well. Don't use an Expense adjustment for a short payment the customer still owes either. Leave that balance open and collect it, or use your approved write-off process.
Common questions
Why doesn't my payment adjustment reason show up in the Name list?
The Payment Adjustments subtab only offers reasons that are active, have an Account, and have Payment selected under Available at Transaction Types. The four reasons NetSuite provides start without an account, so they stay out of the list until you give them one. Open the reason from Setup > Accounting > Accounting Lists and check all three.
Should I use a Revenue or an Expense payment adjustment?
Use Revenue when more money came in than the invoice, like a card surcharge the customer paid. Use Expense when less came in because a processor or bank kept a fee. Revenue reasons post to an income account and Expense reasons post to an expense account.
How do I record a fee the card processor kept?
Create an Expense reason that posts to your fee expense account. Enter the net amount deposited as the Payment Amount, apply the full invoice, and add the fee as a payment adjustment. The net amount plus the fee equals the invoice, and the GL Impact debits the fee expense account.
Why not leave the surcharge as an unapplied payment?
An unapplied amount stays on the customer as a credit, so it shows up as money you owe them until someone clears it with another transaction. The payment adjustment books the 37.20 as surcharge income on the same payment, and Unapplied goes to 0.00.
Does the invoice close when I use a payment adjustment?
Yes, when the applied amount covers the whole balance. In this example A/R is credited 1,240.00, the full invoice, so INV-4471 is paid in full. A short payment the customer still owes should stay open instead of being covered with an Expense adjustment.
Where do I see the accounting for the adjustment?
Open the saved payment's GL Impact subtab, or use Actions > GL Impact. The adjustment has its own line on the reason's account, with the reason name as the memo. In this example that's 4620 Card Surcharge Income, credited 37.20, with the memo Card Surcharge.