Integration of plasma and pulsed light or ultraviolet has been investigated for microbial decontamination of foods. However, no studies have reported the microbial disinfection of particulate food using a large-scale system integrating the treatments. In the present study, a large-scale plasma jet-pulsed light-ultraviolet (UV)-C (PPU) system has been developed for the microbial decontamination of particulate foods. The effects of PPU treatment on the inactivation of natural mesophilic aerobic bacteria and yeast and molds of rice germ and the quality properties of rice germ were evaluated at various operation times (3, 5, 7, and 10 min) and sample amount (200, 500, 1,000, and 3,000 g). The efficacy of microbial inactivation of PPU treatment was enhanced with increasing treatment time and decreasing sample amount, and the maximum reduction was observed at 7 min with 200 g samples. The number of the natural bacteria and yeast and mold was reduced to 1.0 and 2.0 log CFU/g from an initial number of 5.7 and 3.7 log CFU/g, respectively. Compared to the individual treatments by atmospheric pressure plasma jet (APPJ) and intense pulsed light (IPL), PPU treatment synergistically inactivated microorganisms while not altering the color, antioxidant activity, or sensory properties of rice germ. The results of this study suggest the potential use of the large-scale PPU treatment system for the microbial decontamination of rice germ while minimizing alterations in quality.