Self-proclaimed pastor Paul Nthenge Mackenzie is alleged to have incited his followers to starve to death in order to "meet Jesus" in a case that shocked the world.
Mackenzie was arrested in April last year after bodies were discovered in a forest near the Indian Ocean coast.
His pre-trial detention has been extended on several occasions as investigations draw out.
"Upon thorough analysis of the evidence, the director of public prosecutions is satisfied that there is sufficient evidence to prosecute 95 suspects," the DPP's office said.
The move comes a week after a court gave authorities 14 days to prosecute the former taxi driver or release him.
Mackenzie and his co-accused will face 10 charges including murder, manslaughter and terrorism.
They will also be charged with "subjecting a child to torture", the prosecutors said.
It was not immediately clear when the 95 suspects would appear in court, but prosecutors said they undertook "to expeditiously prosecute the matters".
Autopsies have revealed the majority of the victims died of hunger. But others, including children, appear to have been strangled, beaten or suffocated. To date, 429 bodies have been located.
The grim discoveries, in what has been dubbed the "Shakahola forest massacre", prompted the government to flag the need for tighter control of fringe denominations.
Kenya has a history of self-declared pastors and movements.
A Senate commission of inquiry reported in October that Mackenzie had faced charges back in 2017 for his extreme preaching.
"[But] the criminal justice system failed to deter the heinous activities of Paul Mackenzie in Shakahola," it said.
He was acquitted of charges of radicalization in 2017 for illegally providing school teaching. He rejected the formal educational system that he claimed was not in line with the Bible.
In 2019, he was also accused of links to the death of two children believed to have been starved, suffocated and then buried in a shallow grave in Shakahola forest. He was released on bail pending trial.
A largely Christian nation, Kenya seeks to regulate unscrupulous churches and cults that dabble in criminality.
There are more than 4,000 churches registered in the East African country of 53 million people, according to government figures.