Molecular imprinting of polymers is a concept for the synthetic formation of structurally organized materials providing binding sites with molecular selectivity. Compared to biological receptors, these polymeric recognition systems have the advantage of superior chemical and mechanical stability with potential applications in areas such as biomimetic catalysis and engineering, biomedical analysis, sensor technology, or the food industry. In particular, molecularly imprinted polymers (MIPs) providing selectivity for biorelated molecules are gaining substantial importance. In this context, a self-assembly approach for the synthesis of imprinted polymers against the flavonol quercetin is presented, which is exemplary for the biologically relevant group of flavonoid compounds. The creation of synthetic selective recognition sites for this biomolecule is demonstrated by comparing the separation capabilities of imprinted and nonimprinted polymer particles for several structurally related molecules via high-performance liquid chromatography experiments. The developed quercetin-MIP enables selective extraction of quercetin even from complex mixtures, demonstrating the potential for designing biomimetic recognition materials with improved selectivity for biomolecules with tunable functionality at a nanoscale.