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.
For more information, visit GuideStone.org/TaxGuide