The study was conducted to utilize kinnow residues (peel and pomace) and its peel phytochemicals extracted using supercritical fluid extraction, for the preparation of functional cookies. The Wheat flour was replaced with dried kinnow peel and pomace powder at 5, 10, 15, and 20% level of substitution while the phytochemicals extracted were added at 1, 2, 3, and 4% level of substitution respectively. The results showed that the cookies formulated with 10% peel, 5% of pomace, and 4% of phytochemicals obtained the best sensory scores. Cookies with the highest overall acceptability were further analyzed for Physico-chemical, phytochemical and storage studies. Supplementation with kinnow peel and pomace improved crude fiber, ash, and L value of cookies while spread ratio decreased. Supplemented cookies showed a significant increase in the DPPH and FRAP values. Cookies containing peel phytochemicals showed the highest phenolics (12.02 ± 0.11 mg gallic acid equivalent/g), Flavonoids (0.47 ± 0.06 mg quercetin equivalents/g), and carotenoids (0.76 ± 0.03 mg/100 g) followed by cookies containing peel and pomace respectively. The supplemented cookies possessed higher oxidative stability than the control [containing artificial antioxidant Butylated hydroxyanisole (BHA)] over a storage period. Thus it can be concluded that kinnow waste can be utilized as an ingredient for making functional cookies with improved shelf life.