Display omitted •A magnetic pine cone gel beads (MPCB) based adsorbent was successfully prepared.•Single and binary adsorption systems of Cu(II) and Cr(VI) were investigated.•High adsorption capacity of 69.8 mg.g−1 for Cu(II) and 132.5 mg.g−1 for Cr(VI).•Modeling of isotherms by statistical physics and competitive Langmuir model.•Adsorption mechanism of Cr(VI) and Cu(II) onto MPCB was elucidated. Recently, the use of magnetic sorbents has gained a spread attention due to their eco-friendly characteristic, ease of separation and low cost. Herein, a novel biocomposite sorbent magnetic pine cone gel beads (MPCB) was synthetized and investigated for the single and the simultaneous removal of Cu(II) and Cr(VI) from aqueous solution. Pine cones waste materials were first magnetized with Fe3O4 nanoparticles then were encapsulated in calcium gel beads. The physicochemical properties of the prepared MPCB were characterized via scanning electron microscopy-energy-dispersive X-ray spectroscopy (SEM-EDX), X-ray diffraction and Fourier transform infrared spectrometry (FTIR) analysis. The influences of pH, contact time and initial concentration of metal ions on the sorption process were examined. The adsorption mechanism was investigated; it mainly involved complexation/chelation with surface functional groups, electrostatic interaction and ion exchange. A physical model was adopted to attribute new physico-chemical interpretations of the adsorption mechanism. The kinetic results showed good correlation with pseudo second-order model and the equilibrium data were fitted well to the Langmuir isotherm model with maximum adsorption capacity of 68.64 and 212.22 mg g−1 for Cu(II) and Cr(VI) respectively. In the multi-components system, both competitive and synergistic effects were observed. An antagonism effect was exerted by Cu(II) ions on Cr(VI) sorption while Cu(II) adsorption was not affected and even slightly enhanced by the presence of Cr(V) ions. The competitive sorption behavior of metal ions was analyzed by the modified competitive Langmuir model which provides good fit for the Cu experimental data. This study proves that the MPCB hold great promise for using as effective sorbent for potentially toxic metals remediation.