Urban soil accumulates significant contents of heavy metals (HMs), which is a risk to human health and considered as a hindrance for the development and expansion of concerned areas that required to be having simple and field applicable remediation mechanisms with diverse applicable concerning location. A magnetic nanocomposite is fabricated by spherical magnetic ceramsite coated with nanocarbon spheres (MCCS) and functionalized by polyethylene glycol (PEG) for the removal of HMs such as lead Pb(II) and hexavalent chromium Cr(VI) from the contaminated soil. Mesoporous and functionalized magnetic nanocomposite named MCCSPG having plenty of hydroxyl and carboxyl groups are obtained. Box–Behnken design and desirability function are used to optimize maximum adsorption efficiency with three independent factors pH, initial concentration of HMs and initial concentration of MCCSPG. The maximum Langmuir adsorption capacity of MCCSPG is 10.18 mg/g for Pb(II) and 10.05 mg/g for Cr(VI). The pseudo-second-order is fitted the best R² (0.98) for adsorption kinetics. The MCCSPG showed good reusability efficiency six times and collected from the soil via an external magnetic separation system. Short-term and long-term benefits of MCCSPG are also discussed in the topsoil that facilitates its potential applicability for the in situ remediation strategy.