We describe experiments on trapping of atoms in microscopic magneto-optical traps on an optically transparent permanent-magnet atom chip. The chip is made of magnetically hard ferrite-garnet material deposited on a dielectric substrate. The confining magnetic fields are produced by miniature magnetized patterns recorded in the film by magneto-optical techniques. We trap Rb atoms on these structures by applying three crossed pairs of counter-propagating laser beams in the conventional magneto-optical trapping (MOT) geometry. We demonstrate the flexibility of the concept in creation and in-situ modification of the trapping geometries through several experiments.