Once your payroll is finalised, you can pay employees using your preferred payment method and report the details to HMRC in a FPS submission.
If after submitting the FPS file to HMRC you find that there has been an overpayment and you may need to recall the BACS file or receive the refund from the employee(s) by another method, then this must be submitted to HMRC on a further FPS. You cannot, however, create a negative BACS payment to the bank and therefore you will need to recoup the overpayment by other means. You must do this by creating a further payment run.
