Self-proclaimed pastor Paul Nthenge Mackenzie, who has already been charged with terrorism, manslaughter as well as child torture and cruelty, is alleged to have incited hundreds of his acolytes to starve to death in order to "meet Jesus".
On Tuesday, Mackenzie and 29 other suspects pleaded not guilty to 191 counts of murder, including of three infants, according to court documents seen by AFP.
A 31st suspect was deemed to lack the mental fitness to stand trial and ordered to return to the Malindi High Court in a month's time.
Autopsies revealed that the majority of the 429 victims had died of hunger. But others, including children, appeared to have been strangled, beaten or suffocated.
The case, dubbed the "Shakahola forest massacre", led the government to flag the need for tighter control of fringe denominations.
A largely Christian nation, Kenya has struggled to regulate unscrupulous churches and cults that dabble in criminality.
Court documents have described Good News International Ministries founded by Mackenzie as "an organised criminal group (which) engaged in organised criminal activities", leading to the death of hundreds of followers.
According to a chargesheet filed last month at the Tononoka Children's Court in the port city of Mombasa, Mackenzie and 38 other suspects "wilfully and intentionally" denied food to children as young as six years old and whipped others with thorny sticks.
Apart from abuse and neglect, some children were also removed from school and denied their right to an education, the chargesheet said.
Questions have been raised about how Mackenzie managed to evade law enforcement despite a history of extremism and previous legal cases. A Senate commission of inquiry reported in October that the father of seven had faced charges in 2017 for extreme preaching.
He was acquitted of charges of radicalisation in 2017 for illegally providing school teaching after rejecting 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. He was released on bail pending trial.
There are more than 4,000 churches registered in the East African country of 53 million people, according to government figures. Previous efforts to regulate religious institutions in Kenya have been fiercely opposed as attempts to undermine constitutional guarantees for the division of church and state.