Sprouts-related outbreaks have risen due to increased raw sprouts consumption. To minimize such cases, chemical sanitations are applied. While chlorine is commonly used, concerns with its effectiveness and health implication have prompted researchers to seek alternatives. Peroxyacetic acid (PAA) has shown efficacy in inactivating foodborne pathogens on fresh vegetables, and hence could be considered as an alternative. Thus, the objective of this study was to compare the efficacy of chlorine and PAA in inactivating Escherichia coli O157:H7, Listeria monocytogenes, Salmonella spp., and natural microflora on mung bean sprouts. Resistance of non- and acid-adapted pathogens to these sanitizer treatments was also evaluated. Un-inoculated and inoculated sprouts were treated with chlorine at 106, 130 and 170 ppm and PAA at 25, 51 and 70 ppm for 90 and 180 s at room temperature. Overall, the greater log reductions were obtained with the increase in the sanitizer concentration. For 180 s, chlorine treatment at 170 ppm reduced 2.0, 1.3, 1.5, 0.9-logs and PAA treatment at 70 ppm resulted in 2.3, 1.8, 2.1, 1.1-log reductions for non-adapted E. coli O157:H7, L. monocytogenes, Salmonella spp., and natural microflora, respectively. These results revealed that the efficacy of PAA was significantly better than or similar to that of chlorine. For acid-adapted cells, these sanitizer treatments were less effective with the ranges of 1.0–1.2-log reductions for chlorine and 1.1–1.6-log reductions for PAA compared to non-adapted cells, indicating that acid-adapted cells were more resistant to the sanitizing treatment. These data suggest that PAA may replace chlorine in the disinfection of mung bean sprouts and that acid-adapted pathogens should be used to design an effective sanitizing strategy.