Sweet potato is an important food crop in many part of the world that provides essential nutrients and also contains useful phytochemicals with chemopreventive potentials. Although sweet potato peels, which may contain some nutrients and phytochemicals are usually discarded before consumption of the tubers. Therefore, this present investigation seeks to compare the nutraceutical potentials of peels and flesh from white and purple skinned sweet potato. The evaluated antioxidant indices (DPPH radical scavenging capacity, ABTS radical scavenging capacity, reducing power, total phenol, total flavonoid and inhibitory action against lipid oxidation) were higher in peels of the studied potato compared to the flesh. The HPLC-DAD analysis revealed presence of some phenolic compounds (gallic acid, catechin, chlorogenic acid, caffeic acid, caffeic acid derivative, ellagic acid, epicatechin, rutin, isoquercitrin, quercitrin), with higher level of each identified compounds in the peels. The result of the proximate indices (%) revealed a higher value of carbohydrate in the flesh and a higher value of fat, protein and ash in peels of the evaluated sweet potato. The result also showed a higher amount of some of the evaluated minerals (Zn, Fe, Cu, Ca, Mg, Mn) and amylose-amylopectin ratio (white skinned sweet potato: 11.94, purple skinned sweet potato: 13.67) in peels. The result of this investigation showed that that leaving the potato skin intact during processing will enhance the nutraceutical potentials which could be explored in the management of free radical mediated disorders.