Just to be clear on gifts to a pastor, the IRS allows gift of up to $16,000 to ANY individual without a tax liability on either the giver or receiver. So, if an individual gives a pastor $1000, it is considered a gift and does not have to be included in the pastor's tax income.
W-2 or 1099...but not Both by: Vickey
You do NOT want to issue a W-2 and a 1099 to the same individual in the same tax year. It would raise a red flag with the IRS.
How you would "handle" those donations would depend on HOW he received them. If he received them "personally" and they did NOT go thru church records, he is responsible for reporting that "income" on his personal tax return.
If they were received thru the church and ran thru church donation and accounting records ...you would run the "payment" of those donations thru his payroll, so the total amounts would appear in Box 1 of his W-2 along with his regular salary.