Paul Nthenge Mackenzie and 38 other suspects have pleaded not guilty to charges including beating and deliberately starving children, according to Mombasa court documents.
Mackenzie, who has previously been charged with terrorism and manslaughter, allegedly incited his followers to starve to death to "meet Jesus", AFP reported.
A court in the coastal city of Malindi is expected to decide on February 6 whether the self-proclaimed pastor is mentally fit to stand trial.
Mackenzie was arrested in April last year after bodies were found in the Shakahola forest near the Indian Ocean.
Autopsies revealed that most of the 429 victims had starved to death. But others, including children, were found to have been beaten or drowned.
The indictment in the case, which was heard at the Tononoka Juvenile Court in the city of Mombasa, said the crimes took place between 2020 and 2023 in Shakahola forest, where the Mackenzie cult gathered.
The accused "willfully and deliberately" withheld food from six-year-old children and whipped others with barbed sticks, court documents said.
In addition to the abuse and neglect, some children were suspended from school and denied their right to education.
Mackenzie also pleaded not guilty to terrorism and manslaughter.
The gruesome incident, dubbed the "Shakahola forest massacre", has shown that the government needs to tighten its control of radical sects.
Questions have been raised about how Mackenzie managed to evade law enforcement despite his extremist past and previous legal cases.
The Senate's investigative committee reported that Mackenzie was accused of preaching extremist rhetoric in 2017.
Mackenzie, who rejected the formal education system, which he claimed was not biblical, was acquitted of charges of illegal teaching and radicalization in 2017.
In 2019, Mackenzie was also charged in connection with the deaths of two children in Shakahola who were believed to have been starved, drowned and then buried in a shallow grave, but was released on bail pending trial.