Hello, digitail.
We have to make sure you turn on your discount feature in QBO so you can apply it to the invoice. Let me guide you on how to do it:
- Click the Gear icon.
- Select Account and Settings.
- Go to Sales.
- In the Sales form content section, click the pencil icon to edit it.
- Mark the Discount box.
You have two options in adding a discount it will depend on your preference, either Discount percent or Discount value.
Discount percent, as its name states, applies a percentage discount on the total amount on an invoice.

Discount value is straightforward in the sense that whatever value you input on the box will be the discount of the total amount on the invoice.

You can also refer to this article for the steps on how you can add a discount box: Add a discount to an invoice or sales receipt in QuickBooks Online. This includes the steps on how you can apply a discount with a fixed price.
Let me know if there's anything else you need regarding applying discount on the invoice and I'll get back to you. Take care!