Food spoilage is a routine challenge in food production. Saccharomyces cerevisiae is a major contaminating microorganism associated with fruit pulps and juices. Our study demonstrated the effect of a plasma corona discharge on S. cerevisiae viability, membrane permeability, and morphology when the cells were prepared in both dry and wet modes. The S. cerevisiae viability was examined as a function of the duration of plasma exposure, the sample’s distance from the treating head, initial cell concentration, and yeast suspension volume. The results showed a linear correlation between the exposure duration and the CFU/mL in both dry and wet modes. When the initial yeast concentration was 106 CFU/mL, complete eradication in the dry and wet modes occurred after 45 and 240 s, respectively. Exposure of different initial concentrations of S. cerevisiae to plasma in dry (20 s) or wet (90 s) mode led to 2 to 3 orders of magnitude reduction. In both modes, there was total eradication when the initial cell concentration was about 103 CFU/mL. The cell-membrane permeability was examined using a flow cytometer and the fluorescent dye propidium iodide (PI). Plasma treatment in the dry mode for 30 and 45 s led to 51% and 76% PI-positive cells. Similar results were obtained in the wet mode but with a longer exposure for 120 and 240 s, respectively. Atmospheric plasma may provide disinfection technology for the food industry in a short process without heating.