A down payment on a home may be excluded from income as a housing allowance, assuming it does not cause the regular limits to be exceeded.
Example: Reverend Black made a $50,000 down payment on a home. His church designated $55,000 of his $60,000 salary as a housing allowance. Reverend Black had other housing expenses of $10,000, but the fair rental value of the home (furnished, including utilities) was $25,000. He can only exclude $25,000 because the fair rental value was less than the church-designated amount or his actual expenses, including the down payment. If he had made a down payment of $12,000, his total housing expenses would have been $22,000. He could have excluded $22,000 because that amount is lower than the church-designated amount and the fair rental value.
For more information, visit the Ministers' Tax Guide