Green routes for remediation of heavy metals are worldwide challenges to overcome pollution problems on one hand and control the adverse impact of chemicals on the other hand. Biosorption is one of the most effective methods for removing lower level of heavy metals. The idea to apply natural resources as a green method for removal of heavy metals, this route has no adverse impacts on the environment. This study investigated the ability of chemically modified Ziziphus spina-christi stones (ZSCs) as agriculture by-products to perform the biosorption of Pb(II), Zn(II) and Cd(II) ions from wastewater in a single and ternary metal system. The characteristic functional groups of chemically modified ZSCs were analyzed by Fourier transform infrared. In comparison with acidic ZSCs, alkali-modified ZSCs by KOH was more effective and enhanced the removal efficiency of ZSCs. Using Langmuir isotherm, the maximum adsorption capacity on the modified ZSCs for Pb(II) was 9.06 mg/g, for Zn(II) obtained by using ZSC–citric acid was 4.19 mg/g and 5.38 mg/g for Cd(II) as obtained by using ZSC–H2O2. The molecular electrostatic potential, which was calculated at B3LYP/6-31G(d,p), indicated that each metal is di-hydrated, forming a complex with two units of amino acids. This mechanism demonstrated the uptake process by ZSCs.