Room temperature atmospheric plasma treatments are widely used to activate and control chemical functionalities at surfaces. Here, we investigated the effect of atmospheric pressure plasma jet (APPJ) treatments in reducing atmosphere (Ar/1‰ H2 mixture) on the photoluminescence (PL) properties of single crystal ZnO nanorods (NRs) grown through hydrothermal synthesis on fluorine-doped tin oxide glass substrates. The results were compared with a standard annealing process in air at 300 °C. Steady-state photoluminescence showed strong suppression of the defect emission in ZnO NRs for both plasma and thermal treatments. On the other side, the APPJ process induced an increase in PL quantum efficiency (QE), while the annealing does not show any improvement. The QE in the plasma treated samples was mainly determined by the near band-edge emission, which increased 5–6 fold compared to the as-prepared samples. This behavior suggests that the quenching of the defect emission is related to the substitution of hydrogen probably in zinc vacancies (VZn), while the enhancement of UV emission is due to doping originated by interstitial hydrogen (Hi), which diffuses out during annealing. Our results demonstrate that atmospheric pressure plasma can induce a similar hydrogen doping as ordinarily used vacuum processes and highlight that the APPJ treatments are not limited to the surfaces but can lead to subsurface modifications. APPJ processes at room temperature and under ambient air conditions are stable, convenient, and efficient methods, compared to thermal treatments to improve the optical and surface properties of ZnO NRs, and remarkably increase the efficiency of UV emission.