Quercetin (QC) is one of the most prominent dietary antioxidants present in vegetables/fruits, specifically in onions that rank second in consumption following tomato. QC with proven health benefits is now largely utilized as a nutritional supplement. In this work that aims to isolate QC from red onion peels forming a huge agricultural waste, a QC-molecularly imprinted polymer (QC-MIP) in a molar ratio of 1:4:20 (QC:4-vinylpyridine:ethylene glycol dimethacrylate) was prepared thermally through bulk polymerization. Molecularly imprinted solid phase extraction (MISPE) procedures were applied for the selective pre-concentration and purification of QC from both red onion peel methanolic extract with 58% recovery and from the extract hydrolyzate with 86% recovery. The hydrolysis process increased both the QC amount as expected and the recovery yield due to changing matrix components. The results demonstrated that onion peel can easily and efficiently be converted to a valuable product, QC, using QC-MIP as SPE sorbent.