With payrolls, it is good practice to create a liability account called something like Payroll Clearing. Instead of taking the net pay directly to the bank account, credit the Payroll Clearing account. Then take up the actual payments from the Bank Statement or cheques and debit the Paroll Clearing account. It is a bit of extra processing, but If you short pay someone and the payroll run is correct, you simply pay the short fall, debit payroll clearing from the bank statement or cheque, and this will then clear the outstanding credit amount (which would have been the difference). This practice also helps you to avoid a situation where you make an ad hoc wages payment and debit the wages account and forrget to process it through payroll. In this case it would now sit as a debit on the payroll clearing account and you would pick up the fact that you had not processed the payroll for this amount when you reconcile the account. This is good practice even if you create an EFT file from the payroll as it avoids the second scenario.
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