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Squalene, a triterpenoid compound possessing excellent bioactivities, is not being utilized as a functional food ingredient due to its high susceptibility to oxidation. In the present study, the feasibility of chitosan-whey protein as an efficient wall material for squalene encapsulation using spray drying technique was attempted for functional food applications. The encapsulation efficiency of the squalene powder was found to be 75.4 ± 0.22% whereas other physico-chemical properties such as moisture content, flowability, solubility, peroxide value, etc. have shown satisfactory results. The thermogravimetric analysis showed that chitosan-whey protein was able to retain the thermal stability of squalene up to a temperature of 422 °C. Furthermore, the functional food application of the encapsulated squalene in a bakery product (cake) exhibited significantly (p < 0.05) better properties in terms of oxidative stability …