A new effective adsorbent, 3-aminopropyltrimethoxysilane functionalized magnetic sporopollenin (MSp@SiO2NH2) based silica-coated graphene oxide (GO), (GO@SiO2-MSp@SiO2NH2) was successfully synthesized and applied for the first time in the removal of hazardous Pb(II) ions from aqueous solution. The properties of the composite were characterized using Fourier-transform infrared spectroscopy (FTIR), thermogravimetric analysis (TGA), field emission scanning electron microscopy (FESEM), energy-dispersive X-ray spectroscopy (EDX) and vibrating-sample magnetometery (VSM). Evaluation of GO@SiO2-MSp@SiO2NH2 adsorption performance at optimum conditions revealed that the adsorbent has a maximum adsorption capacity of 323.5 mg/g for Pb(II) using 50–200 mg/L initial Pb(II) ions concentrations. Initial and final concentrations of Pb(II) ions in aqueous solution were analyzed using graphite furnace atomic absorption spectroscopy (GF-ASS). The adsorption behavior of Pb(II) ions onto GO@SiO2-MSp@SiO2NH2 was studied using Langmuir, Freundlich and Temkin isotherms models. The values of coefficient of determination showed that the adsorption best fitted the Langmuir model (R2 = 0.9994). Kinetic studies suggested that the adsorption of Pb(II) ion followed a pseudo-second-order rate model (R2 = 1.00) and thermodynamic studies revealed that the adsorption process is endothermic and spontaneous. The effect of co-existing ions on Pb(II) ion adsorption were also studied and found to have considerable effects only at higher matrix concentration. The adsorbent can be reused up to ten times and retain its good adsorption capacity. In addition, GO@SiO2-MSp@SiO2NH2 showed great potential for Pb(II)removal from industrial wastewater samples.