We observed nanoscale distribution of subgap excitations induced by Ga-ion beam processing in β-Si3N4 via electron energy-loss spectroscopy performed using a monochromated (0.1 eV) and aberration-corrected scanning transmission electron microscope. A sufficiently low operating voltage (30 kV) was selected to suppress background caused by Cerenkov loss in β-Si3N4 with a high refractive index. By further combining crystallinity, composition, and bandgap measurements, we found that defects excited at the band edge (6 eV) and lower energies (3 eV) exhibit different dependence trends with respect to crystallinity. The proposed technique was verified to effectively distinguish between various amorphous materials.