A new nanocomposite (HBS) was prepared based on humic acid, biochar, and silica using the coprecipitation method for methylene blue dye removal from industrial wastewater. The humic acid, biochar, and silica are produced from compost, tomato residual, and Rice husk feedstocks. The HBS nanocomposite was characterized by FTIR, XRD, SEM, Zeta potential, BET, and SEM-EDX. The mean surface area, average pore volume, average crystal size, and surface charge of the nanocomposite were 41.68 m2/g, 4.20 nm of 9.95nm, and negatively charged surface with nanosized crystals, respectively. The batch experiments included the effect of dose, initial concentration, pH, connect time, temperature, and isothermal model. The optimum conditions for removing methylene blue from wastewater are 50 mg of HBS, 100 mg/L (initial concentration), pH 9, and contact time of 60 min at room temperature. The adsorption process was endothermic and fitted with the Langmuir model. The maximum adsorption capacity was 16.23 mg/g. The negative value of ∆Go indicates the spontaneous process of adsorption. The HBS nanocomposite was successfully regenerated in three cycles for the removal of MB.