Yes, you can. When recording a payment for an invoice, you will find an option to add transaction fees.
You can record transaction fees in absolute amounts or as a percentage of the cash received.
The transaction fee option might be useful in some scenarios such as:
Your payment provider charges you a fee when you receive funds from your customers.
When you record a transaction fee for an invoice payment, the transaction fee charged is deducted from the Cash Received amount, giving Net Cash Received.
On the invoice details, the payment amount shown in the invoice total summary will reflect the Gross Cash Received or the cash received before fees.
You can add a VAT/GST included in the fee.
You just need to select a tax profile and Juan will calculate the actual fees and the included GST/VAT.
On the general ledger, you should see a record reflecting the transaction fees charged under the expense account (e.g. Transaction Fees & Charges) that you have selected when recording a transaction fee.
If you have added GST/VAT included in the transaction fees, you should see an additional record for the included GST/VAT under the Input GST Receivable account.
