A reader wrote in saying he had recently started working for a small church, stating he needed help in setting up a housing allowance item for his pastor.
You can add a clergy housing allowance as an "addition item" to your employee’s payroll profile, but these payments can range in taxability and set-up. You must be certain to confirm the taxability of the housing allowance with the accountant or tax advisor for your church or the pastor in question.
As a general rule, you can refer to the chart shown below for details on set-up in QuickBooks payroll:
Payroll Clergy Housing Allowance Table
Hopefully this will help you accomplish the outcome you're seeking.