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Besides employment by churches, and synagogues, clergy employed by other types of organizations may be eligible to receive a tax qualified housing allowance also.
In Boyd v. Commissioner, 42 T.C.M. 1136 (1981), a chaplain employed by a police department received a housing allowance designated by a federation of churches that organized the chaplaincy program. This was because the organization was recognized.
There have been private letter rulings which determined that hospitals, retirement homes, and other types of entities may be qualified organizations for purposes of designating a housing allowance. Private letter rulings cannot be used by any one except the person that requested them to argue a position but they do help.
The housing allowance is not taxable for income tax but it is for Self Employment (which is SS and medicare) so the CPA should have completed the SE tax form for for you.
If they did not, have them amend your filing.
I am checking back to see if you contacted the CPA about that filing.