Developing novel and effective antimicrobial methods is imperative for ensuring food safety during commercial apple production. In the present study, the bactericidal effects of dipping apples into a combination of bisulfate of soda (BS) and peracetic acid (PAA) was investigated using Listeria innocua as a surrogate inoculated to whole apples. Decontamination treatments included washing with water as control, chlorine at 150 ppm, 1% BS with 60 ppm PAA, 3% BS with 60 ppm PAA, and 3% BS with 60 ppm PAA and a surfactant sticker (0.1% Tween). After dipping with antimicrobial solutions for 2 min, apples were stored over a time period of up to 2 weeks and L. innocua survivors were enumerated from apple core collected from 30 min, 1 day, 7 days, and 14 days. Washing with water showed little antimicrobial effect; only a 1.52 log10-cycle reduction was observed after 14 days (L. innocua population at 0 and 14 days: 5.96 and 4.44 log CFU/g, respectively), indicating that washing was not sufficient to control L. innocua on apple. When apples were treated with chlorine, L. innocua populations were reduced to 3.58, 2.19 log CFU/g after 1 and 7 days, respectively, but afterward increased to 3.80 log CFU/g at 14 days of storage. In contrast, the combined treatment of BS and PAA resulted in marked bactericidal activities (log10-cycle reduction by 1% BS with 60 ppm PAA after 30 min, 1, 7, and 14 days: 2.57, 2.70, 5.45, and 4.30 log CFU/g, respectively; log10-cycle reduction by 3% BS with 60 ppm PAA: 3.66, 5.24, 5.50, and 5.56 log CFU/g). Adding a surfactant sticker did not result in a significant increase in antimicrobial effects thus 3% BS with 60 ppm PAA would be an optimal treatment for use in the apple industry. This combined decontamination method has important advantages including consumer and industry preference for natural compound, its potential application to industry, and cost-effectiveness. The combined treatment of BS and PAA may be a useful decontamination method for improving the microbiological safety in whole apples.