Sweet potato is an important staple, and it is mainly known for its contribution of β-carotene in human diet. The effects of cultivar and habitat on this pigment and other nutritional characteristics of the crop still require investigation. In this study, three locally bred cultivars of sweet potato, two of which are orange-fleshed, were grown in three different agro-ecological areas to determine soluble sugar content, β-carotene, and total antioxidants of roots. In addition antioxidant activity, total carotenoids, and chlorophyll content were determined in edible leaves. Reducing sugars, β-carotene, total antioxidants capacity, total carotenoids, and chlorophyll content were significantly affected by environmental conditions. The location at lower altitude and closer to the coastline showed high evapotranspiration, thus reducing sugar content, antioxidant activity, and phytonutrients in both storage roots and leaves. Absence of water stress in agro-ecological locations further inland and at higher altitudes was associated with an increase in these compounds. Free radical scavenging activity of DPPH was higher in the storage roots (610.49 µmoles TE/100g) than in the leaves (426.06 µmoles TE/100g); nevertheless, opposite results were found for the ferric ion reducing activity (FRAP). The deep orange-fleshed cultivar A45 contained high β-carotene (15 mg/100g), which is enough to meet RDA for vitamin A. There is evidence of agro-ecological effect on sweet potato nutritional value.