Different pathogenic microorganisms have been reported to cause sprouts-associated outbreaks. This work aimed to evaluate the effect of corona discharge plasma jet (CDPJ) on disinfection of the natural bio-contaminants of broccoli seed and also studied the plasma effect on sprout seed germination rate and physico-chemical properties of sprouts. Aerobic bacteria, molds and yeasts, B. cereus, E. coli, Salmonella spp. were detected on the broccoli seed surface. After 0-3 min treatment using CDPJ, the detected microorganisms were reduced in the range of 1.2-2.3 log units. Inactivation patterns were better explained using pseudo-first-order kinetics. The plasma treatment of seeds up to 2 min exhibited positive effects on the germination rate and the seedling growth. The physico-chemical and sensory characteristics of sprouts were unaffected due to the CDPJ treatment of their respective seeds. The CDPJ can potentially be used for microbial decontamination of broccoli seeds.