1099 or W-2 for working minister

Housing Allowances are never recorded on a 1099.

Those payments as considered “nontaxable” in regards to federal income taxes…even though they are subject to self-employment taxes… if a minister has not “opted out”of the SS System.

You can record those HA payments in BOX 14 on a W-2 as that box is simply an informational box.

Or you can simply issue him a “notification” letter from the church stating how much “housing allowance” the church gave him in a calendar year.

I have an example of that letter on this page:

https://www.freechurchaccounting.com/how-do-i-write-a-housing-allowance-letter-for-tax-purpose.html