Authorities say Mackenzie, the head of the Good News International Church, ordered his followers in southeastern Kenya to starve themselves and their children to death so that they could go to heaven before the world ended.
More than 400 bodies were uncovered over the course of months of exhumations across tens of thousands of acres of forest, making this one of the world's worst cult-related tragedies in recent history.
Prosecutors say they will charge 95 people in total on counts of murder, manslaughter, terrorism and torture.
A lawyer for Mackenzie, who has been in custody since police started unearthing bodies in the forest, has said the self-styled pastor is cooperating with the investigation.
During a hearing in the coastal town of Malindi, a judge granted a prosecution request to conduct mental health assessments of the 31 defendants before they are formally charged and enter pleas in two weeks.
Mackenzie, dressed in a white-and-blue-striped polo shirt, sat largely expressionless alongside his fellow defendants in the courtroom.
Prosecutors have attributed delays in bringing charges to the gruelling and delicate task of locating, exhuming and autopsying so many human remains. Some of Mackenzie's other followers were rescued, emaciated, from the forest.
People with knowledge of the cult's activities told Reuters last year that Mackenzie planned the mass starvation in three phases: first children, then women and young men, and finally the remaining men.
A former taxi driver, Mackenzie forbade cult members from sending their children to school and from going to hospital when they were ill, branding such institutions as Satanic, some of his followers said.
He was convicted in December of producing and distributing films without a license and sentenced to 12 months in jail.
