Glucuronidation is a well-established biotransformation process that modifies the physiological and pharmacological properties of small molecules, making it a valuable tool for enhancing the chemical diversity of natural compounds in drug development. However, the chemical synthesis of glucuronides is often complex, time-consuming, and environmentally unsustainable. To overcome these challenges, plant uridine diphosphate (UDP)-glucuronosyltransferase (UGT)-mediated glucuronidation, using transformed yeast, offers a selective and efficient alternative for producing flavonoid glucuronides. This study aimed to conjugate quercetin with glucuronic acid by stably co-transforming Saccharomyces cerevisiae with plant UGTs (UGT78A11 and UGT88D7) and rat UDP-glucose-6-dehydrogenease. The UGT78A11 and UGT88D7 selectively conjugated quercetin at specific positions, producing quercetin-3-O-glucuronide and quercetin-7-O-glucuronide, respectively. The whole-cell biotransformation platform effectively leverages the regio-selectivity of UGT78A11 and UGT88D7 to convert polyhydroxy secondary metabolites into monoglucuronides with promising yields, thereby enhancing the availability and physiological potential of these glucuronides.