The flavonol quercetin in plants and foods occurs predominantly in the form of glycoside whose sugar moiety affects the bioavailability and the mechanism of its biological activities. The antiproliferative activities of quercetin derivatives such as quercetin aglycone, quercetin-3-β-D-glucoside (Q3G), and rutin were compared using six different cancer cell lines including colon, breast, hepatocellular, and lung cancer. The IC50 value of Q3G ranged between 15 and 25 μM in HT-29, HCT 116, MCF-7, HepG2, and A549 cells. In these five cell lines, Q3G showed the most potent growth inhibition, whereas rutin showed the least potency. Transformation of rutin to Q3G was conducted by controlling α-L-rhamnosidase and β-D-glucosidase activities from crude enzyme extract of Aspergillus niger. Carbon sources during culture and transformation conditions such as pH, temperature, and heat-stability were optimized. After 4 h biotransformation, 99% of rutin was transformed to Q3G and no quercetin was detected. This study presented an efficient biotransformation for the conversion of rutin to Q3G which was newly shown to have more potent antiproliferative effect than quercetin and rutin.