Recently, protein purification methods have a very wide area of research. Many of these methods are both expensive and multi-stage methods, that are needed in specific equipment. In this study, biopolymer coated magnetic nanoparticles, carboxymethyl cellulose (CMC) and chitosan (CH) coated Fe3O4 (magnetite) nanocomposites, are used in a new purification process. The structure of the synthesized magnetic nanocomposites were characterized by Fourier transform infrared (FTIR) spectrometry, X-ray diffraction (XRD), scanning electron microscope (SEM), transmission electron microscope (TEM), thermogravimetric (TGA) analysis and zeta potential for surface charge of magnetic nanocomposites. Molecular weight and purification degree of peroxidase were estimated with SDS-PAGE. Peroxidase enzyme was purified a yield of 82.55% with carboxymethyl cellulose and 76.72% with chitosan using this method. (C) 2016 Elsevier B.V. All rights reserved.