Yes. A housing allowance may be excluded from income for federal income tax purposes, but not for SECA tax purposes.

Example: Reverend Smith's designated housing allowance is 40% ($16,000) of his $40,000 salary. Assuming he can exclude the full amount designated by the church, he will not report the $16,000 as income for federal income tax purposes. But he will have to count the $16,000 as income for purposes of SECA taxes.

If you are retired, housing allowance may be excluded from income for SECA tax purposes.

For more information, visit the Ministers' Tax Guide