Ion-beam effects on bulk silica at low temperature have been studied with the aim of understanding the routes and mechanisms leading from the initial generation of free carriers and self-trapped excitons (STEs) to the production of two stable defect structures in irradiated silica, non-bridging oxygen hole centers (NBOHCs) and oxygen deficient centers (ODCs). Ion beam induced luminescence (ionoluminescence, IL) spectra were obtained using 3 MeV H, 3.5 MeV He, 19 MeV Si, and 19 MeV Cl ions and a range of cryogenic irradiation temperatures from 30 to 100 K. The kinetic behavior of three emission bands centered at 1.9 eV (assigned to NBOHCs), 2.1 eV (assigned to the intrinsic decay of STEs), and 2.7 eV (assigned to ODCs) reveal the physical origin of these emissions under intense electronic excitation. The creation of NBOHCs is governed by a purely electronic mechanism. The kinetics curve of the NBOHC band shows two main contributions: an instantaneous (beam-on) contribution, followed by a slower fluence- and temperature-dependent process correlated with the concentration of STEs. The beam-on contribution is proportional to deposited ionization energy. The growth of the ODC band is linear in fluence up to around 2 × 1012 cm−2. The growth rate is independent of temperature but proportional to the number of radiation-induced oxygen vacancies per ion, showing, unambiguously, that the 2.7 eV emission can be associated with ODCs created in an excited state.