Isoflavonoid representatives such as genistein, daidzein are high potent anti-cancer, anti-bacterial, anti-oxidant agents. It have been demonstrated that methylation of flavonoids enhanced the transporting ability, which lead to facilitated absorption and greatly increased bioavailability. In this paper, genetically engineered Escherichia coli was reconstructed by harboring E. coli K12-derived metK encoding S-adenosylmethionine (SAM) synthase (accession number: K02129) for enhancement of SAM as precursor and a Streptomyces avermitilis-originated SaOMT2 (O-methyltransferase, accession number: NP_823558) for methylation of daidzein and genistein as preferred substrates. The formation of desired products via biotransformation including 7-O-methyl-genistein and 7-O-methyl-daidzein were confirmed individually by chromatographical data such as HPLC, LC-TOF-MS and NMR ( H and C) as well. Furthermore, substrates concentration, incubation time and media parameters were optimized using flask culture. Finally, the most fit conditions were applied for fed-batch fermentation with scale up to 3 L (working volume) to obtain the maximum yield of the products including 164.25 μM (46.81 mg/L) and 382.50 μM (102.88 mg/L) for 7-O-methyl genistein and 7-O-methyl daidzein, respectively. In particular, potent inhibitory activities of those isoflavonoid methoxides against the growth of cancer line (B16F10, AGS and HepG2) and endothelical (HUVEC) cells were investigated and demonstrated. Taken together this research work described the production of isoflavonoid-7-O-methoxides by E. coli engineering, improvement of production, characterization of produced compounds and preliminary in vitro biological activities of the these flavonoids being manufactured. This article is protected by copyright. All rights reserved.