An environment friendly green synthesis of iron oxide nanoparticles using the seed coat extract of B.flabellifer was investigated. The nanoparticles were characterized using XRD, UV–vis spectroscopy, FTIR, TGA, SEM and EDS. The x-ray diffraction spectrum showed the formation of crystalline inverse spinel magnetite nanoparticles with crystallite size of 35 nm and the UV–vis absorption recorded characteristic peak at 352 nm for iron oxide nanoparticles. The surface functionalization of the nanoparticles was confirmed from the various functional group peaks present in the FTIR spectrum and the thermal decomposition of the synthesized nanoparticles from TGA. The morphological study using SEM showed the formation of hexagonal shaped, well dispersed nanoparticles. The cytocompatibilty of the iron oxide nanoparticles was studied using MTT assay and haemolytic analysis. The antimicrobial activity of the nanoparticles against E. coli, S. aureus, B.subtilis, Shigella, A.niger and Candida albicans were measured and the nanoparticles showed significant activity against all the microorganisms which increased with increase in the nanoparticle concentration. The free radical scavenging activity of the nanoparticles against DPPH, Hydrogen peroxide and hydroxyl radical was performed which showed efficient antioxidant activity.