Ginsenoside Rg3, a known anti-cancer agent, is usually prepared by enzyme-mediated and acid hydrolysis of ginsenoside Rb1 and Rd. In this study, we used the bacterium Cellulosimicrobium cellulans sp. 21 to transform Rb1 into Rg3. When Rb1 was used as the sole substrate, the transformation products included Rg3, Rh2, C-K and PPD. However, when Rb1 and Re were mixed, the yield of Rg3 was significantly higher, indicating that Re attenuates the activity of beta-1,2-glucosidase secreted by C. cellulans sp. 21. beta-1,2-glucosidase hydrolyzes the beta-1,2-glucose moiety at the C-3 position of Rb1, but Re dose not modify enzymes that produce Rg3 by hydrolyzing glucose at the C-20 position in aglycon. We also tested the inhibitory effects from various ginsenosides on beta-1,2-glucosidase, and discovered that sugar chains played key roles in inhibiting beta-1,2 glucosidase activity, whereas aglycones of protopanaxadiol and protopanaxatriol had little inhibitory effects. Some sugar chains with different linkages, such as C-20, C-3 and C-6, exhibited different inhibitory effects. Overall, our findings demonstrate that a combination of substrates, in addition to microorganism-secreted enzymes, can be used for selective bio-transformation. This approach provides a novel strategy for natural product preparations via microbial transformation.