Nutrient management of sweet potato requires more attention for sustainable yield increase. A study evaluating the yield and nutrient use efficiency of two sweet potato varieties (Butter milk and TIS 87/0087) in a nutrient omission trial, was conducted at the farm station of the National Root Crops Research Institute (NRCRI), Nyanya sub-station, Abuja, Nigeria, during 2023 farming season. Nitrogen, P and K fertilizers were applied at the rates of 100, 40 and 120 kg ha−1, respectively. Fresh root yield ranged between 9.63 to and 31 t ha−1 with mean agronomic efficiency of 46, 113 and 33 kg fresh yield of storage roots per kg of N, P and K applied and average partial factor productivity of 194, 447 and 132 kg N, P and K ha−1, respectively for both varieties. Storage root yield responses to applied N, P and K fertilizers were 8 and −7.6, –2 and 5.2, 4 and 3.4 t ha−1 for Butter milk and TIS 87/0087, respectively. The fertilizer contribution rate of N, P and K towards yield formation was 28, −7 and 14%, respectively for Butter milk and −73, 50 and 33% of N, P and K, respectively for TIS 87/0087. The results show that Butter milk recorded more yield than TIS 87/0087. In summary, it was suggested that planting high yielding varieties with optimum crop nutrient management practices, i.e. fertilizer recommendation based on indigenous soil fertility knowledge or crop nutrient requirement, with strategies to match the nutrient input with target yield and demand, should be adopted to improve yield and nutrient use efficiency in sweet potato production.