The present invention provides a substrate processing apparatus capable of suppressing mutual contamination and/or damage of the insides of ion beam generators arranged opposite each other via a substrate, and a magnetic recording medium manufacturing method. A substrate processing apparatus according to an embodiment of the present invention includes a first ion beam generator that applies an ion beam to one surface to be processed of a substrate W, and a second ion beam generator that applies an ion beam to another surface to be processed, which are arranged opposite each other via the substrate W, and an area of a first grid in the first ion beam generator, and an area of a second grid in the second ion beam generator, each area corresponding to an opening of the substrate W, are occluded.