Magnetic nanoparticles NiFe2O4 was synthesized and covered in the silicate lattice of (3-Aminopropyl) trie-thoxysilane (APS) by the sol-gel process. Subsequently, the EDTA-dianhydride was attached to the amino surface of magnetic nanoparticles (MNPs) during the nucleophilic attack. This polycarboxylic layer trapped the high level of nickel ions for selective bonding to the His-tagged recombinant protein. The surface of MNPs was investigated by TEM, XRD, SEM (EDSA), VSM, BET, FT-IR and zeta potential analysis which characterized the size, chemical lattice, morphology, magnetic strength, specific surface area, functional groups and charge of the surface of nanoparticles. The performance and validity of the nanoparticles were studied by the purification of His-tagged green fluorescence protein (His-GFP). Also, the safety of proposed Ni-MNPs in the purification procedure of His-tagged proteins for pharmaceutical applications was proved by the determination of the nickel leakage level in the purified final protein using atomic absorption spectroscopy. In vitro cytotoxicity of Ni-MNPs and trace metal ions was investigated by the MTS assay technique. In addition, the comparison of biological activity in purified protein (GM-CSF) and commercial sample did not show any toxic effect.