No, the expenses for housing are not allowed as a deduction on your self employment tax (Schedule SE). The key to the housing allowance is that as long as you spend at least as much on housing costs as the amount of the housing allowance then no personal income tax applies. If you spend less than your allowance on your housing costs, the difference is subject to personal income tax.
Examples of housing expenses:
- Mortgage Interest
- Insurance
- Property Taxes
- HOA Dues
- Utilities
- Maintenance (repairs, lawn care, snow removal, etc).
Keep in mind that the church must designate in advance a housing allowance or it will not be considered as housing.