Biofortification of zinc (Zn), iron (Fe) and selenium (Se) in crops could be affected by environmental factors such as soil salinity and phosphorus supply levels, as well as by the genotypic effect. Two pot experiments were conducted with one examined the effects of P supply and salinity on plant growth and Zn, Fe and Se uptake in wheat, and the other examined genotypic differences in Zn, Fe and Se accumulation among 20 wheat genotypes. The results of the first pot study showed significant interactive effects between P supply and salinity on Zn, Fe and Se accumulation. Increasing salinity at the same P supply level increased shoot Zn concentrations, but significantly decreased total shoot Zn amount owing to decreased aboveground biomass. An increased accumulation of total shoot Fe and Se in P-added treatments, relative to the no-P treatments, was mainly due to increased aboveground biomass. The results of the second pot study showed substantial genotypic variations in Zn, Fe and Se accumulation; principal component analysis (PCA) suggested that agronomic traits and nutrient accumulation were controlled by independent genetic mechanisms. These results indicated that the amount of P supply is a key factor regulating biomass and accumulation of Zn, Fe and Se in certain saline soils; the sizable genotypic difference in Zn, Fe and Se accumulation observed in salinised conditions has provided potential scope for genetic improvement by breeding strategies.