Eggs are one of the most commonly consumed food items. Currently, chlorine washing is the most common method used to sanitize shell eggs. However, chlorine could react with organic matters to form a potential carcinogen, trihalomethanes, which can have a negative impact on human health. Plasma-activated water (PAW) has been demonstrated to inactivate microorganisms effectively without compromising the sensory qualities of shell eggs. For this study, various amounts (250, 500, 750, or 1000 mL) of PAW were generated by using one or two plasma jet(s) at 60 watts for 20 min with an air flow rate at 6 or 10 standard liters per minute (slm). After being inoculated with 7.0 log CFU Salmonella Enteritidis, one shell egg was placed into PAW for 30, 60, or 90 s with 1 or 2 acting plasma jet(s). When 2 plasma jets were used in a large amount of water (1000 mL), populations of S. Enteritidis were reduced from 7.92 log CFU/egg to 2.84 CFU/egg after 60 s of treatment. In addition, concentrations of ozone, hydrogen peroxide, nitrate, and nitrite in the PAW were correlated with the levels of antibacterial efficacy. The highest concentrations of ozone (1.22 ppm) and nitrate (55.5 ppm) were obtained with a larger water amount and lower air flow rate. High oxidation reduction potential (ORP) and low pH values were obtained with longer activation time, more plasma jet, and a lower air flow rate. Electron paramagnetic resonance (EPR) analyses demonstrated that reactive oxygen species (ROS) were generated in the PAW. The observation under the scanning electron microscope (SEM) revealed that bacterial cells were swollen, or even erupted after treatment with PAW. These results indicate that the bacterial cells lost control of cell permeability after the PAW treatment. This study shows that PAW is effective against S. Enteritidis on shell eggs in a large amount of water. Ozone, nitrate, and ROS could be the main causes for the inactivation of bacterial cells.