Cationic doping of ZnO nanorods has gained increased interest as it can lead to the production of materials with improved luminescent properties, electrical conductivity and stability. We report on various Mo-doped ZnO powders of nanorods synthesized by the hydrothermal growth method. Further annealing or/and cold hydrogen or oxygen plasma modification was applied. The atomic structure of the as-grown and plasma-modified rods was characterized by X-ray diffraction. To identify any possible changes in morphology, scanning electron microscopy was used. Paramagnetic point defects were investigated by electron paramagnetic resonance. In particular, two new types of defects were initiated by the plasma treatment. Their appearance was explained, and corresponding mechanisms were proposed. The changes in the luminescence and scintillation properties were characterized by photo- and radioluminescence, respectively. Charge trapping phenomena were studied by thermally stimulated luminescence. Cold plasma treatment influenced the luminescence properties of ZnO:Mo structures. The contact with hydrogen lead to an approximately threefold increase in intensity of the ultraviolet exciton-related band peaking at ~3.24 eV, whereas the red band attributed to zinc vacancies (~1.97 eV) was suppressed compared to the as-grown samples. The exciton- and defect-related emission subsided after the treatment in oxygen plasma.