Traditional soybean (Glycine max L.) breeding has improved seed yield in high-input agricultural systems, under high nitrogen (N), phosphorus (P) and potassium (K) supply. The seed yield improvements under non-P supply and the seed protein and mineral content dilution by yield improvement were evaluated in 18 soybean cultivars released from 1995 to 2016 in south-east China. Soybean varieties were grown under rainfed conditions in the field under 0 and 35 kg P ha−1 in four sites: Dafang and Shiqian in the growing season of 2017 and Dafang and Puding in the 2018 season. The seed yield, seed protein content and nine seed nutrition concentration were examined. Soybean seed yield increased with the year of release at rates of 5.5–6.7 g m−2 year−1 under 35 kg P ha−1 and 3.9–4.8 g m−2 year−1 under non-P supply in the four experiments. The increase resulted from increases in the number of filled-pods and total seed number rather than from single seed weight and number of seeds per pod. Seed protein content and seed nutrition concentration has not changed with the year of release under 0 and 35 kg P ha−1. Grain yield was positively correlated with the seed Fe concentration. The cultivar superiority of seed yield, seed P, Zn and Ca concentration was negatively correlated with their static stability coefficient. Traditional soybean breeding increased yield under both P and non-P supply, without affecting seed protein content and mineral concentrations. A trade-off between high seed yield and seed P, Zn and Ca concentration and their stability under different environments was shown.