Vendor credits sync one-way from Bill.com to QuickBooks Desktop, and vendor credit application syncs one-way from Bill.com to QuickBooks Desktop.

Vendor Credits are not applied via the sync until a bill is paid in full

• If a Vendor Credit covers the FULL amount of a bill, the $0 payment marking the bill as completely paid in bill.com must sync to QuickBooks Desktop for the vendor credit to be applied. 

• If a credit only covers part of a bill's balance, the credit will not be applied in QuickBooks Desktop until the remainder of the bill is paid, even if the credit is applied in Bill.com.

Manually applying credits in QuickBooks Desktop is not suggested in most cases; if the credit is manually applied in QuickBooks Desktop, the payment(s) itself associated to the same bill(s) will error, as the sync will not be able to apply credit at the same time as the payment(s).