A method of processing a substrate in an apparatus including a substrate holder which holds the substrate, an ion source which emits an ion beam, a neutralizer which emits electrons, and a shutter which is arranged between a space in which the ion source and the neutralizer are arranged and a space in which the substrate holder is arranged, and configured to shield the ion beam traveling toward the substrate, includes adjusting an amount of electrons which are emitted by the neutralizer and reach the substrate holder during movement of the shutter.