"Clergy Self-Employment": Which option should I choose if my church withheld federal income taxes on my W-2? I receive a housing allowance, but is not included on my W-2.

[Opus 17]

Did the church withhold income taxes (box 2) or also social security and medicare taxes (box 4 and 6)?

[Opus 17]

And you are a clergy member hired to perform religious duties (lead worship, perform sacraments, etc.)?

[David-P]

Yes, I am a clergy member and the church withheld funds in box 2 only.

[Opus 17 · Accepted solution]

So that's no problem.  Enter the W-2 as is, check the box on the page of special circumstances for religious wages.  Check the box for pay SE tax on wages and housing allowance, enter the amount of the allowance and your qualified expenses.  You pay SE tax on wages plus housing allowance, and you pay income tax on wages only.  You will get credit for the withholding, and will either owe more tax or get a refund, depending on your other tax situations.  If you made additional estimated tax payments, record them on the Deductions page under "Estimates and other taxes paid."