You will have to wait until you get to “Bank Deposit” tab to apply discount given against this invoice.

Let’s start the process:

• #1 Receive Payment tab (Create + plus sign > Customers > Receive Payment)
  Show full Invoice payment on “Received Payment” screen, but select Deposit to as “Undeposited Funds” account.
• Note: Received Payment form is currently blank and incomplete at this time to handle other debit and credit adjustments if necessary.
• Sending it to Undeposited Funds account (rather than directly to bank account) and make other adjustments (like Discounts taken or Merchant Fees) from Bank Deposits screen where they have “Add New Deposits” field

• # 2 Bank Deposit tab (Create + plus sign > Other > Bank Deposit
• Select Customer Payment
• Go to “Add New Deposits” section
• Account = Discount given (Contra Income Account type)
• Amount = Discount Amount (Enter negative amount)
• Check box “Track returns for Customers” and select Customer under Customer column (optional). This will help to track a discount taken by a customer.

QuickBooks Online: How can I apply discount taken by a customer on payment received