Self-proclaimed prophet Shepherd Bushiri and his wife Mary handed themselves over to police in Lilongwe, Malawi on Wednesday.
The Gauteng High Court in Pretoria on Wednesday issued warrants of arrest for the Bushiris, who fled South Africa and went to their home country of Malawi last week.
The Bushiris broke their bail conditions when they left under mysterious circumstances.
The Enlightened Christian Gathering church leader, his wife and three others are accused of fraud involving around R102 million.
The couple was out on R200 000 bail each when it emerged they had not appeared for their Friday check-in with police - a requirement in terms of their bail conditions.
On Saturday, Bushiri said in an interview that they had fled because they believed their lives were in danger in South Africa and they would not get a fair trial.
On Wednesday, Bushiri said in a statement that he would be presenting himself before law enforcement agencies on Wednesday morning to "legally explain and defend the decisions that I made to come to Malawi".