Due to recent changes in the QuickBooks Online API, there is now only one way to sync discounts into QuickBooks Online, as QuickBooks Online no longer allows 3rd party apps to create a negative line item in QuickBooks.
This setting is very simple to ensure you have enabled, and consists of one setting you need to check in QuickBooks Online.
In QuickBooks Online, go to the gear in the top right > Account & Settings > Sales > Sales Form Content, and ensure the checkbox for Discounts is checked.
Additionally, we recommend you also enable the Shipping box here as well, as this will enable a Shipping subtotal field in your QuickBooks invoice/sales receipts for us to sync shipping costs into. If this Shipping setting is not on, we would sync shipping as a line item.
Once this setting is on, then when an order is synced to QuickBooks Online from WooCommerce, the discount in the WooCommerce Order would show correctly in the “Discounts” subtotal field in your invoice/sales receipt.