The four men entered the church in Port Elizabeth looking for the local pastor to pray for them for a pending court appearance.
When they realized he was not there they then stole a cellphone, laptops and an undisclosed amount of money.
Police spokesperson Alwin Labans told the BBC that the suspects were armed with knives.
“They found a 26-year-old man in the prayer room and demanded prayers from the pastor. They then pulled their knives and robbed him. They have yet to be identified but we are investigating the matter,” he said.
The men then took the church member to the kitchen while they plundered the church, in search of whatever valuables they could find.
Police say the robbery is being investigated.