Note: you don't exclude anything from your income. You might have to include something.
Your housing allowance must be designated in advance and in writing by your church or denomination. It should not be reported as part of your box 1 W-2 taxable wages. That is, it is already excluded from income. Then, you add up your qualified housing expenses. If your housing expenses are less than the housing allowance, you must add back the excess housing to your income (include it in your income). If your housing expenses are more than the housing allowance, you don't get an additional deduction or exclusion.
If your housing allowance is not already excluded from your taxable wages by your church, there is no legal way to deduct or exclude your housing costs. The allowance must be set up properly and excluded by your church, the question is whether or not you need to add anything back.
