Magnetic iron oxide nanoparticles (MION) for protein binding and separation were obtained from water-in-oil (w/o) and oil-in-water (o/w) microemulsions. Characterization of the prepared nanoparticles have been performed by TEM, XRD, SQUID magnetometry, and BET. Microemulsion-prepared magnetic iron oxide nanoparticles (ME-MION) with sizes ranging from 2 to 10 nm were obtained. Study on the magnetic properties at 300 K shows a large increase of the magnetization ~35 emu/g for w/o-ME-MION with superparamagnetic behavior and nanoscale dimensions in comparison with o/w-ME-MION (10 emu/g) due to larger particle size and anisotropic property. Moringa oleifera coagulation protein (MOCP) bound w/o- and o/w-ME-MION showed an enhanced performance in terms of coagulation activity. A significant interaction between the magnetic nanoparticles and the protein can be described by changes in fluorescence emission spectra. Adsorbed protein from MOCP is still retaining its functionality even after binding to the nanoparticles, thus implying the extension of this technique for various applications.