Most clergy should have a W-2 because they are common law employees of their church, but because they are exempt from tax withholding, boxes 2-6 should be blank. If the W-2 looks different, post the details here because it probably means the church is doing the payroll wrong. The box 1 wages are subject to self-employment tax on schedule SE.
Clergy can also have schedule C income for side gigs, whether religious (performing weddings and funerals, ad hoc hospital chaplain, etc) or secular.
A housing allowance is non-taxable for income taxes, but it is taxable for self-employment taxes. The housing allowance should not be reported on the W-2 at all, unless it is reported in box 14, which is a memorandum field that has no impact on the tax return.
line 2 of schedule SE should represent the total of the pastor’s box 1 wages, housing allowance, and any schedule C income. When using TurboTax, there is an interview step that will ask about a pastor’s housing allowance and correctly add it to schedule SE. After entering the W-2, click "religious wages" on the page of special circumstances. You will be asked about the housing allowance amount, and whether to pay SE tax on "wages only", "housing allowance only" or "both" -- both is always the correct answer. The other answers are only needed if the pastor needs to correct a mistake made by their church's payroll person.
If you are preparing taxes by some other method, you will have to look to your own method to ensure that both wages and housing allowance are subject to SE tax.
