It's easy to record discounts that you have provided your customers that aren't listed on the invoice (for early payment, for example) You can do so when adding a payment for the invoice:

  • Open the invoice and match it to the payment received.

  • Since the invoice amount is higher than the amount received, you will be asked if the difference is an expense. 

  • Confirm this and select "Discount" as the category. 

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