Self-proclaimed pastor Paul Nthenge Mackenzie and 94 other suspects pleaded "not guilty" to charges of radicalization.
The cult leader was also charged with "organized criminal activity," according to documents from the Mombasa court seen by AFP.
Mackenzie is alleged to have incited his acolytes to starve to death in order to "meet Jesus" in a case that horrified the world.
He was arrested last April after bodies were discovered in the Shakahola forest near the Indian Ocean, with autopsies revealing that the majority of the 429 victims had died of hunger.
But others, including children, appeared to have been strangled, beaten or suffocated.
Mackenzie's pre-trial detention in the coastal city of Mombasa was extended on several occasions as the prosecution asked for more time to probe the case.
But last week a court warned the authorities that it would release the former taxi driver unless charges were filed within 14 days.
The grisly case, dubbed the "Shakahola forest massacre," prompted the government to flag the need for tighter control of fringe denominations.