Flavonoids are the plant secondary metabolites considered to be pharmaceutically important for the human health. However, instability and very low oral bioavailability of dietary flavonoids are causing hindrances for their maximum utilization as therapeutics and commercialization. In this paper, genetically engineered Escherichia coli harboring SaOMT2-MetK was employed for regiospecific 7-O-methylation of naringenin, apigenin and quercetin. The formation of desired products via biotransformation were confirmed individually by chromatographical data such as HPLC and LC-TOF-MS and the purified compounds were tested for biological activities. We also demonstrated greater pharmaceutical potential of sakuranetin, genkwanin and rhamnetin as anti-carcinogenic, anti-melanogenic and anti-angiogenic agents, compared to their unmethylated forms. Taken together this research work best describes the pilot scale fermentation for the production, methylation for improvement of biological activities and glycosylation for enhancement of solubility of the flavonoids being tested.