The man who was shot was thought to have brought a brick into the church and attempted to attack the pastor.
It has been reported that 25-year-old Deante Smith had previously posted on his Facebook page that the pastor had gotten his wife pregnant, according to The Detroit News.
Police sources said that detectives have been looking into an alleged affair between Keon Allison and Deante Smith's wife.
Assistant Chief Steve Dolunt said police believe Mr Smith was shot around 15 minutes after the start of the 1:30pm Sunday service at the church.
It has also been reported that the pastor is cooperating with authorities and has not been arrested.
Speaking to reporters, Deja Ward, Mr Smith's sister, said that her brother had gone to the church to find closure with the pastor before beginning counselling with his spouse.
The couple had previously lived with the pastor, and Mr Smith had considered him a mentor and called him dad, according to his sister.
Mr Smith died from his injuries in hospital.
Steve Dolunt, Assistant Police Chief, told the Free Press: "The pastor had had issues with the man before.
"He had been threatening him to do bodily harm.
"He walked into the service and went after the pastor with a brick.
"The pastor pulled out his Glock and fired several shots. I think he hit him 4 or 5 times, and the man died."
