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Puerarin, an important isoflavonoid from the edible root of Pueraria lobata, shows multiple bioactivities but suffers from low bioavailability. In this study, a new whole-cell catalytic method for acylation modification of puerarin was developed. Among the 12 strains tested, Aspergillus oryzae showed the highest catalytic activity and selectively catalyzed acylation of puerarin at the 6″-hydroxyl group. The organic solvents used significantly influenced the catalytic efficiency of the cells. In the green solvent 2-methyltetrahydrofuran, the reaction showed high substrate conversion (92.5%) and regioselectivity (95.8%), with results similar to those with tetrahydrofuran (94.2% and 98.5%, respectively) under optimal conditions. The monoester products showed higher liposolubility in comparison to puerarin, and those with C3-C8 fatty acid chain lengths showed evidently improved antioxidant activity toward erythrocyte hemolysis. Considering the operational stability of the cells and efficiency of the scaled-up reactions, this method is efficient and cost effective, with promising applications in the health food industry.