One of the nonthermal methods is the atmospheric pressure cold plasma (APCP). In this study, the effect of cold plasma on the reduction of Escherichia coli bacteria and qualitative properties of sour cherry juice, including total phenolic content (TPC), total anthocyanin content (TAC), and vitamin C, were investigated. Independent variables included plasma exposure time (1, 5, and 9 min), applied field intensity (25, 37.5, and 50 kV/cm), feeding gas oxygen content (0%, 0.5%, and 1%), and sample depth (0.5, 1, and 1.5 cm). The results show that increased oxygen content in argon has the greatest effect on the reduction of bacteria, and plasma exposure decreased 6 logarithmic periods of E. coli bacteria in sour cherry juice. Optimization results showed when all bacteria were eliminated by plasma, TPC remained unchanged, and TAC and vitamin C decreased by 4% and 21%, respectively, while thermal methods increased TPC by 23% and decreased TAC and vitamin C by 26% and 77%, respectively. These results indicate that, compared with conventional thermal methods, sour cherry juice pasteurization using APCP has little effect on the juice qualitative properties, and this method can serve as a suitable alternative to conventional thermal methods.