That's in relation to the deaths of 429 of his followers whose bodies have been exhumed from the Shakahola forest.
His court appearance in the southeastern city Mombasa came the day after a hearing in a separate court in the coastal town of Malindi.
There a judge ordered that Mackenize and 30 of his associates undergo mental health evaluations before they are charged with murder in relation to 191 of the deaths.
The terrorism-related charges, however, are the first to be brought against Mackenzie since he was arrested in April after bodies started to be discovered.
Mackenzie and his co-defendants denied the charges.
Authorities say Mackenzie, head of the Good News International Church, ordered his followers to starve themselves and their children to death so that they could go to heaven before the end of the world.
A lawyer for Mackenzie has said the self-styled pastor is cooperating with the investigation.
Prosecutors in Mombasa and Malindi say they will also charge the 95 people on counts of manslaughter and torture.
