Orlando Gentry was charged Tuesday with assault, possession of a firearm, unlawful use of a weapon and carrying a loaded firearm in the shooting.
Kansas City police say the 29-year-old Gentry fired the shots during a confrontation Sunday at the House of Refuge church.
One of the bullets grazed Montell Bruce in the head and then he fell through a window in the sanctuary. Bruce was treated and released.
The Kansas City Star reports that Gentry told investigators he got into a fight at the church but denied having a gun.
Online court records do not show that Gentry has an attorney.