This study investigated plasma-activated water (PAW) as a sanitizer for the washing of sprouts. Alfalfa sprouts, broccoli sprouts, and clover sprouts were washed with PAW, chlorine (CL, 200 ppm), or deionized water. The inactivation of aerobic mesophilic microorganisms and inoculated E. coli DH5α was evaluated. The quality of sprouts was assessed based on visual color change (ΔE) and plant tissue damage (electrolyte leakage, EL). Significant reductions of 1–2 log CFU/g in aerobic mesophilic microorganisms were achieved by PAW and Cl on clover sprouts and alfalfa sprouts. Reductions of E. coli ranging between 1.4 ± 0.4 log CFU/g and 3.5 ± 0.9 log CFU/g were achieved by PAW in all the sprouts (original counts: 6.4 to 8.1 CFU/g), which were comparable to Cl except for the case of alfalfa sprouts where Cl achieved the highest inactivation. No significant quality difference in terms of visual color change or electrolyte leakage was observed in sprouts washed by PAW and Cl.