A series of novel 4-(3-(4-benzylpiperazin-1-yl) propoxy)-7-methoxy-3-substituted phenyl-2H-chromen-2 one (7a–7j) were synthesized by the reductive amination of 7-methoxy-3-phenyl-4-(3-piperizin-1-yl-propaxy)chromen-2-one (6) with different substituted aromatic aldehydes by using sodium cyanoborohydride in methanol. The newly synthesized compounds were purified and their structures were characterized by IR, 1 H NMR, 13C NMR, and mass spectroscopy. The representative analogs were screened for in vitro antimicrobial activity. The compounds exhibited significant antibacterial and antifungal activity as that of standards. The data was further compared with structure-based investigations using docking studies with the crystal structure of oxidoreductase (1XDQ and 3QLS) protein organisms. The estimated score by genetic algorithm was found to have a good correlation with the experimental inhibitory potency of the derivatives.