Most polyphenols are metabolized by xenobiotic-metabolizing enzymes (XMEs), UDP-glucuronosyltransferases (UGTs), and sulfotransferases (SULTs), which can catalyze the formation of glucuronide and sulfate of polyphenols, respectively. The type of conjugates produced in the body may determine the metabolic fate and the deconjugation process of the polyphenols related to their physiological function. Genetically modified budding yeast, Saccharomyces cerevisiae, having Phase II XMEs, is one of the useful host organisms for the platform of the production of UGT and SULT-dependent polyphenol conjugates, glucuronides, and sulfoconjugates via whole-cell biosynthesis. The enzyme-assisted synthetic system of polyphenol conjugates allows us to promote the supply of various structurally different compounds with convenient and low-cost production. Such an authentic standard for the conjugate may be significantly useful to elucidate the detailed pharmacokinetics and molecular mechanisms underlying the biological activity of polyphenols.