As the primary barrier, the skin is continuously exposed to various chemicals and pollutants. Therefore, it has been regarded as able to metabolize diverse compounds. With growing interest in phytochemicals for personal products and functional foods, understanding their metabolism has become increasingly important. However, studies on their biotransformation at the skin remain poorly characterized. In this study, we aimed to uncover the metabolites of phytochemicals by skin bacteria and mechanisms including the enzymes. Six bacterial strains were obtained from KCTC and cultured with 17 phytochemicals. LC–MS/MS dataset was acquired and analyzed through the GNPS platform using molecular networking to annotate the metabolites. Andrographolide, eupatilin, naringenin, licochalcone A, isoliquiritigenin, and neferine were expected to be metabolized. Notably, to our knowledge, predicted metabolites of licochalcone A by Staphylococcus xylosus had not been reported from plants. From these results, licochalcone A was prioritized for further large-scale purification. While the isolation and purification are still ongoing, one derivative of licochalcone A was identified as a hydrogenated form. We expect that our investigation will contribute to the understanding of the biotransformation of phytochemicals by skin microbiota.