Did the nonprofit issue any 1099s? Just not to him? How were the 990 questions about 1099s answered?

The nonprofit's procedures need to be tightened. They should be getting a W-9 from all independent contractors.before payment is made.

It is not really the independent contractor's responsibility to say "Hey, I need a 1099" although sometimes they will ask. The individual should have been reporting all of his income whether or not he received a 1099.

Is the contractor asking now?