Phosphorus (P) addition ameliorates the adverse effects of water stress on the seed yield of soybean (Glycine max L.). Previous studies focused on the effect of P on root traits, but little information is available on changes to aboveground traits. In this paper, we show how P addition affects shoot traits and reduces the adverse effects of water stress on the yield. Two soybean genotypes, with contrasting aboveground architectures, were grown in pots to compare the canopy architecture, leaf traits, aboveground dry matter accumulation and yield under two water and three P levels. The addition of P to two soybean genotypes, one with a larger number of branches and greater leaf area on the branches than the other, showed that the increased leaf area distribution on the main stem and branches was associated with increased shoot and root dry weights, which were positively correlated with the number of filled pods, seed number and seed yield and negatively correlated with seed size at maturity under well-watered and cyclic water stress treatments. The leaf P concentration at 65 DAS (flowering stage) and leaf photosynthesis measured shortly after re-watering increased with P addition, while the leaf mass area on the main stem at 65 DAS and maturity and on the branches at maturity increased modestly with P supply and water stress. Evidence is presented that P addition can ameliorate the adverse effects of water stress on yield through increased leaf area, leaf function and aboveground shoot production. We conclude that the increased yields of soybean resulting from increased P and water supplies that were previously shown to be associated with increased root growth and function are mediated through increased shoot growth and function, particularly the greater number of sites for pod production.