I think what he is asking is what if the expenses for his housing totals more than what his actual salary is. You obviously can't get paid more than what your salary is (whether it's classified as housing allowance or not), but it is possible to have all 100% of your salary be considered as housing allowance--provided it meets all the requirements of what is deemed housing allowance.
Housing Allowance and Taxes by: Vickey
Are you asking what you should do if your properly documented and approved housing allowance is less than your actual housing expenses?
If you are inquiring about what to do tax-wise ...
the answer is you can only exclude from income tax...not self-employment tax...the lesser of the three amounts mentioned in Anonymous post
You would report the lesser of the above amounts on a Schedule SE on your personal income tax return and pay self-employment tax on it... unless you have been approved to opt out of SS.
housing by: Anonymous
A minister who receives such an allowance must report the lesser of the following amounts on a SE schedule on their personal income tax return:
•The amount actually spent on eligible housing expenses.
•The fair market rental value plus furnishings and utilities.
•The amount officially designated in advance as housing allowance.
There is a ton of info on this on this site be sure to go to the clergy/minister section :0)
Income less than housing costs by: Anonymous in NC
The church approved housing allowance is subtracted from your clergy gross income to determine your taxable income. It is possible that the approved housing allowance is more than the church paid gross income.