Onion peels (OP) are byproduct of food processing industries that poses economic and environmental challenges. However, being rich source of bioactive compounds like Quercetin (Qt), a polyphenolic antioxidant with potential health benefits, harnessing value from such waste can imbibe sustainable practices and protect environment. With this view, the present study targets selective recovery of Qt from OP waste using rationally designed molecularly imprinted polymer (MIP). Density Functional Theory (DFT) was used for the theoretical selection of the best conformer of Qt (template), methacrylic acid (MAA) as functional monomer, ratio of Qt-MAA for getting stable pre-polymerization complex, and to avoid hit and trial experiments. The theoretical results were validated experimentally by synthesizing MIP/ control polymer (NIP) using MAA as functional monomer, EGDMA as a cross-linker and AIBN as initiator. Synthesized MIP/NIP were characterized using various characterization techniques to confirm successful imprinting. Prepared MIP and NIP could effectively rebind the Qt molecule with binding capacity of 46.67 and 20.89 mg g-1 respectively. Furthermore, synthesized MIP could selectively recover 62.81 % of Qt from 1 g of dry onion peel powder. This study can be effectually used for sustainable recovery of Qt in large scale for various foods, cosmetic and pharmaceutical applications.