There is an urgent need to develop efficient and environmentally friendly decontaminants for poultry products. In this study, we aimed to evaluate the practical application of peroxyacetic acid (PAA) as a replacement for sodium hypochlorite (SH) to sterilize fresh chicken carcasses, using microbial, color, and electronic-nose analyses. We evaluated the decontamination effects of different concentrations of PAA and SH on chicken carcasses. The bactericidal effects of PAA at pH 3, 7, and 9, and SH at pH 10, at concentrations ranging from 100 to 500 ppm on coliform bacteria, total bacteria, and Salmonella spp. were evaluated. PAA induced a similar bactericidal effect at lower concentrations than SH. Therefore, at the same concentration and treatment time, PAA showed better bactericidal effects than SH. Although treatment with PAA (pH 3) and SH (pH 10) resulted in considerable discoloration, the degree of discoloration decreased when the pH of PAA was increased to 7 and 9. Therefore, by increasing the pH of PAA, the discoloration effect on chicken carcasses can be reduced without altering the microbial-reduction effect. Electronic-nose analysis showed that the flavor of the chicken was almost unaffected by volatile components at a treatment time < 30 min. Therefore, this study experimentally identified the optimal PAA concentration for the decontamination of chicken carcasses. The study findings provide a theoretical basis for the replacement of traditional bactericides, such as SH, with PAA for the production of poultry products.