A new nanobiosorbent based on cross-linked chitosan magnetic beads modified with methionine-glutaraldehyde schiff’s base (MG-Chi/Fe3O4) was synthesised for removing Cu(II), Pb(II) and Cd(II) from wastewater samples. Fourier transform infrared spectra (FTIR), X-ray diffraction (XRD) analysis, and scanning electron microscope (SEM) have been applied to characterise nanobiosorbent. A variety of parameters influencing uptake behaviours of the metal ions, including pH, adsorbent dose, contact time, initial concentration of the metal ions and desorption conditions were examined and optimised. The pH ZPC of MG-Chi/Fe3O4 was found to be 4.0. Freundlich and Langmuir isotherm models were applied to estimate adsorption mode. The equilibrium data were well fitted with the Langmuir isotherm model. The maximum adsorption capacities for Cu(II), Pb(II), and Cd(II) were 172.4, 175.4 and 163.9 mg g−1, respectively. The adsorption kinetics fitted better with the pseudo-second-order model indicating that chemical adsorption is the rate-limiting step in the adsorption process. The adsorbent (MG-Chi/Fe3O4 nanobiosorbent) performance is maintained for at least 4 adsorption-desorption cycles. Finally, MG-Chi/Fe3O4 nanobiosorbent exhibited high potential to remove the metal ions from Iran Khodro’s wastewater.