Mackenzie is accused of persuading members of his Good News International Church to settle in a remote forest and start fasting in preparation for the end of the world.
Prosecutors have announced that a Kenyan cult leader and 94 others will face charges of murder and terrorism in connection with the deaths of more than 400 people buried in mass graves.
Paul Mackenzie was taken into custody in April following the unearthing of hundreds of corpses, some of which reportedly died of starvation.
The Kenyan authorities say that he and his co-accused will appear in court in Malindi on Wednesday.
The self-styled pastor has rejected any blame for the deaths.
The remains of 429 people, among them children, were recovered from burial sites in Shakahola, a secluded forest about two hours’ drive west of Malindi.
Mackenzie is accused of persuading members of his Good News International Church to relocate there and get ready for the end of the world.
A witness told the BBC that people were instructed in January last year to start fasting so that they could “get to heaven”.
But Mackenzie has claimed that the deaths were not his fault as he shut down his church in 2019. Investigators had requested his detention to be prolonged several times as they pursued their investigation.
They said their probes had now collected enough evidence to charge him and the others with crimes including murder, assault and “facilitating the commission of a terrorist act”.
Of the 95 suspects, 64 were discovered in Shakahola and were initially regarded as victims and transferred to a rescue centre.
However, investigators later discovered that many of them had children who had perished in the forest.
Some of them had provided false names and identities and failed to account for their children.
Mackenzie was found guilty last November of unlawfully operating a film studio linked to his preaching and distributing films without a valid filming licence.
