Moringa oleifera seed and leaf are used traditionally for the treatment of various health problems (among others, hypertension, scrapes, skin infection, diabetes, genitourinary illnesses), and to boost the immune system, as well as to act as a contraceptive. In this study, the antibacterial activity of seed and leaf M. oleifera extracts on three-gram negative bacteria was investigated, and phytochemical analysis for the association of antibacterial activity with the active constituents in the plant was determined. Moreover, understanding of the mechanism of action was achieved by applying the Auto Dock Vina technique. The phytochemical screening of M. oleifera seed and leaf extracts exhibited the presence of alkaloids, carbohydrates, cardioactive glycosides, flavonoids, tannins, phenols, steroids and terpenoids. In silico results revealed that compounds (4-O-caffeoyl quinic acid, 4-(α-L-rhamnopyranosyloxyl)-benzylisothiocyanate); (Isoquercitrin, 4-(α-L-rhamnopyranosyloxy) benzyl glucosinolate); and (Astragalin, 4-(α-L-rhamnopyranosyloxy) benzyl glucosinolate) from leaf and seed have the highest binding affinity and very good interactions with Transcriptional Activator Protein (LasR), Klebsiella pneumoniae carbapenemase (KPC), and Malonyl-CoA-acyl carrier protein transacylase (FabD), respectively.