It has recently been reported that 5α-androst-16-en-3-one (androstenone) is a key compound in body malodors, and that female subjects were more sensitive than male subjects to androstenone. Androstenone is generated by the metabolism of a skin-resident microorganism, Corynebacterium xerosis, and apricot kernel extract (AKE) effectively suppressed this metabolism. In this study, AKE was fractionated according to its suppressive activity on androstenone generation in C. xerosis, in order to confirm its active constituents. (R)-Prunasin and (S)-prunasin, which were nitrile compounds, were isolated and identified as the active constituents in AKE and they strongly suppressed the bacterial metabolism. Amygdaline was also isolated as an (R)- and (S)- mixture. This compound is a typical bioactive ingredient in apricot kernel and the structure has one more glucose molecule with β-1,6 bond in contrast to prunasin. However, amygdalin was not included in the active fraction and it did not have any effect on suppressing androstenone generation. Furthermore, neither prunasin nor amygdalin had any bactericidal effect. In addition, the generation of hydrogen cyanide was not detected from either of them during incubation with C. xerosis in the reaction to generate androstenone. Based on these results, we confirmed that prunasin was the active constituent in AKE suppressing the generation of androstenone. The mechanism did not depend on the inhibition of metalloprotein through the generation of hydrogen cyanide from prunasin. This suppressive effect is possibly based on the tertiary structure of prunasin and the structure may influence the metabolic components that are related to the generation of volatile steroids in skin-resident microorganisms.