Genetic engineering is a potential approach to improve secondary metabolism in plants. In order to elucidate the effect of production of anthocyanin pigment 1 (PAP1) overexpression on the bioactivity of ginseng, we analyzed its antioxidant, antimicrobial, and anti-elastase activities in this study. Our results showed that PAP1 overexpression increased the production of polyphenolic compounds including anthocyanins. The antioxidant, antimicrobial, and anti-elastase activities were stronger in anthocyanin-overproducing ginseng hairy roots (AOX) than in wild ginseng hairy roots. Using a different solvent system (0, 30, 70, and 100% (v/v) EtOH), we revealed that variations in the contents of the polyphenolic compounds were highly correlated with changes in the antioxidant and antimicrobial activities of AOX. The antioxidant, antimicrobial, and anti-elastase effects of AOX highlight genetic engineering as a powerful approach to enhance the therapeutic properties of plants. Our results show that AOX could potentially have various functional applications in the cosmetic and pharmaceutical industries.