The antimicrobial activities of isolated compounds from seed extracts of Moringa oleifera and synergistic antimicrobial efficacy through hybridized complex of organic-inorganic composite materials were studied. The two main components of the Moringa oleifera seed were isolated and determined to be niazimicin and 4-(α-L-rhamnosyloxy)-benzyl isothiocyanate (RBI). The antimicrobial activity of the separated compounds of the Moringa oleifera seed were tested in vitro against 3 bacterial species and 2 fungal species by the paper disc diffusion assay and broth dilution methods. Both compounds showed antimicrobial activity against tested species and RBI was more effective than niazimicin. The MIC of RBI on S. aureus, E. coli, P. aeruginosa, C. albicans, and A. niger was 0.005%, 0.1%, 0.5%, 0.5%, and 0.5%, respectively, while the MIC of niazimicin on S. aureus was 0.1%. Next, we investigated the combined antimicrobial action of mesoporous ZnO and RBI by incorporating the compound within the pore of mesoporous ZnO. The MIC of mesoporous ZnO with RBI on S. aureus, E. coli, P. aeruginosa, C. albicans, and A. niger was 0.001%, 0.01%, 0.5%, 0.1%, and 0.1%, respectively. A synergistic effect of RBI with mesoporous ZnO was shown. From these results, the mesoporous ZnO could act as a reservoir for RBI and mesoporous ZnO with RBI could be used for cosmetic preservatives.