IF you are talking about a parsonage allowance for a pastor or minister, this income is subject to self-employment income, but is not subject to income tax, up to the actual cost of housing. For example, if your actual cost of housing is $15,000 but the housing allowance is $18,000, the remaining amount is added back to taxable income. On the other hand, if actual housing expenses are $18,000 and the parsonage allowance is $15,000, only the $15,000 can be excluded from income and there are no deductions for the other "unused" $3000 of housing expenses.
There are a lot of other rules, pastors should read this,
https://go.efca.org/resources/document/preparing-tax-returns-clergy
A pastor with a housing allowance can certainly file a joint return.
If you are talking about something else, we need to know more details, we don't recognize whatever you are talking about.
