In this study, an attempt has been made to devise a method for a large-scale production of quercetin from a medicinal plant. The natural products are first isolated from plants and then synthesized commercially. During their synthesis, a number of impurities or side products are also formed, most of which are carcinogenic. Plant products have limited side effects. Therefore, they are considered safe to be used for systemic uses. In the Rubus fruticosus fruit, the ethyl acetate extract was loaded to 50 optimized silica gel columns. The effluents of columns were passed through the membrane system for concentration. A 100% recovery was achieved from the drain pipe in case of reverse osmosis membrane when the specified rely of the pilot plant was set on 25% rejection. About 95% recovery was achieved through the NF membrane while the 5% loss in permeate was recovered through magnetic carbon nanocomposite (characterized through a bar magnet, SEM, XRD, and EDX). The equilibrium time of adsorption was 83 min and followed by pseudo-first-order kinetics. The adsorption equilibrium data fitted well to the Langmuir isotherm model. Through the devised method, quercetin was successfully concentrated with high efficiencies; however, further studies are needed to validate the method.