The extreme sensitivity of 2D materials to defects and nanostructure requires precise imaging techniques to verify presence of desirable and absence of undesirable features in the atomic geometry. Helium-ion beams have emerged as a promising materials imaging tool, achieving up to 20 times higher resolution and 10 times larger depth-of-field than conventional or environmental scanning electron microscopes. Here, we offer first-principles theoretical insights to advance ion-beam imaging of atomically thin materials by performing real-time time-dependent density functional theory simulations of single impacts of 10–200 keV light ions in free-standing graphene. Here we predict that detecting electrons emitted from the back of the material (the side from which the ion exits) would result in up to three times higher signal and up to five times higher contrast images, making 2D materials especially compelling targets for ion-beam microscopy. This predicted superiority of exit-side emission likely arises from anisotropic kinetic emission. The charge induced in the graphene equilibrates on a sub-fs time scale, leading to only slight disturbances in the carbon lattice that are unlikely to damage the atomic structure for any of the beam parameters investigated here.