Mark Storms, 46, of Pennsylvania was convicted for the manslaughter of Robert Braxton III, 27, by a jury on Thursday.
The prosecution in the trial said that Braxton had become disruptive in a Sunday service at Keystone Fellowship Church in April.
Storms ordered Braxton to leave, before a scuffle began.
Storms shot Braxton in the shoulder and chest and Braxton was later pronounced dead a few hours later at hospital.
Over 300 worshippers witnessed the shooting.
A parishioner testified at the trial that after being shot twice, Braxton was chased by Storms out of the building.
During the trial, Storms told the court he had been scared for his life.
He claimed that Braxton had entered the auditorium, muttering to himself and shouting at an elderly man.
Storms said: "I didn't know, is this guy a terrorist? Is he on drugs? Does he have some kind of weapon under that jacket that we haven't seen?"
The jury reached there guilty verdict after only a few hours of deliberation.
Storms sentencing will take place at a later date.