Generally it seems it was mostly in areas where Catholicism and Protestantism were in close contact and had compete for believers or in protestant dominated areas.

The Spanish inquisition for the most pairt maintained the medieval view that witchcraft could not exist from a theological perspective and continued prosecuting belief in it as a heresy.

I'm not defending the church, though. They declared witchcraft to be an irrational superstition to delegitimize pagan beliefs a few centuries earlier yet had no qualms about embracing the same beliefs to gain a competitive edge when competing against protestants.