Authorities accuse Mackenzie, head of the Good News International Church, of ordering his followers to starve themselves and their children to death so they could go to heaven before the end of the world.
Police have exhumed hundreds of bodies from mass graves in Shakahola forest in the country's southeast.
The self-styled pastor handed himself in to police in April and has repeatedly been denied bail while investigations continue into the mass deaths.
He has not yet been charged for his alleged role in the deaths or entered a plea.
On Friday Magistrate Olga Onalo found the Mackenzie guilty of operating a film studio, producing films and showing them to members of the public without a valid license.
James Mouko, the accused lawyer said he would appeal against the ruling. Local media reported Mackenzie was convicted and fined for a similar offense in 2017.