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In this study, eco-friendly casein-copper hybrid nanoflowers (CAS-Cu HNFs) were synthesised and their applicability for the removal of Pb(II) and Cd(II) ions was investigated. Hybrid nanoflowers were synthesised by adding CuSO4 solution on casein in PBS medium. According to the evaluation of SEM images, regular nanoflower structures were obtained after the addition of 40 µL of 100 mM CuSO4 and 12 h incubation. Characterisation studies were performed by XRD, SEM-EDX, FTIR and TGA. The effects of contact time, pH, temperature and heavy metal ion concentration on the adsorption performance were investigated. Optimum adsorption was achieved at 60 min contact time and 35 and 30 °C for Pb(II) and Cd(II) ions, respectively. The performance of CAS-Cu HNFs was evaluated by linear and non-linear forms of adsorption isotherms and adsorption kinetics, respectively. The linear Langmuir isotherm model showed compatibility and the maximum adsorption capacity was found to be 769.23 and 156.25 mg/g for Pb(II) and Cd(II) ions, respectively. CAS-Cu HNFs has great potential as an eco-friendly, nanoscale, flower-like, organic–inorganic hybrid nano-flower adsorbent for the effective removal of Pb(II) and Cd(II) ions from aqueous solutions. [ABSTRACT FROM AUTHOR]