Adjustments can be applied to any invoice as part of its line items as shown below.

Open the invoice and and click on the option Adjustments.

The Invoice has to be in Open Invoice Status if you're were to apply any adjustments.

Select the Adjustments and click on Create New button as shown below.

Select the Invoice item and Apply the adjustment Type and amount along with the posting date.

Click on Save as shown below.

The Adjustment which is posted will appear as an line item in the Invoice and the Amount will be deducted from the total amount as shown below.