Ultrasonication, redox-pair generated free radical method and their combination (Ultrasonication/redox-pair method) was used for production of camel whey-quercetin conjugates. FTIR and SDS-PAGE confirmed successful production of whey-quercetin conjugates using ultrasonication and ultrasonication/redox-pair method. FTIR suggested existence of covalent (appearance of new peak at 3399 cm−1) and non-covalent linkages (shifting of peak at 3271 cm−1, 1655 cm−1 (amide I), 1534 cm−1 and 1422 cm−1 (Amide II)) in the whey-quercetin conjugates. Moreover, SDS-PAGE of conjugates produced by ultrasonication as well redox-pair method indicated shifting of protein bands slightly towards high molecular weight due to increase in the mass of proteins due to the binding of polyphenols. All conjugates showed improved techno-functional and bioactive properties in comparison to whey proteins. Conjugates produced through ultrasonication showed smaller particle size, improved solubility, emulsifying and foaming properties while conjugates produced through ultrasonication/redox-pair method depicted superior antioxidant properties in comparison to whey. Furthermore, conjugated samples showed higher inhibition of enzymatic markers involved in diabetes and obesity with highest potential recorded in conjugates produced using ultrasonication. Therefore, ultrasonication can be successfully used individually as well as in combination with redox-pair for production of whey-quercetin conjugates with enhanced bioactive and techno-functional properties.