In the present study, general and versatile method for the functionalization of silica coated Fe3O4 nanoparticles by surface carboxylic group have been established. We have shown that malic acid functionalized magnetic nanoparticles (MA-MNPs) are an effective sorbent material for toxic metals such as cadmium and nickel. This magnetic sorbent was characterized by X-ray diffraction, scanning electron microscope and infra-red spectra. The adsorption of all studied metal ions onto Malic acid functionalized magnetic nanoparticles was found to be dependent on pH. Batch adsorption equilibrium was very fast under optimum conditions and maximum monolayer capacity, Qm, obtained from Langmuir isotherm for Cd2+ and Ni2+ were 81.627 and 63.995mgg−1, respectively at 25◦C. Adsorption data were fitted well to Langmuir and Freundlich isotherm (R2 ≈ 0.99). The malic acid grafted on Fe3O4@SiO2 enhanced the adsorption capacity because of the complexing abilities of the multiple hydroxyl and carboxyl groups with metal ions.