Effective nutrient management considering nutrient interactions is important in order to increase crop yield and improve crop nutrient concentration. The objective of this study was to investigate the effect of P and Zn fertilizers on the yield and nutritional value of flax and durum wheat. A pot culture experiment conducted in a growth chamber using a calcareous clay-loam soil showed that P fertilizers can restrict flax growth by reducing Zn absorption but can increase the seed yield of both crops by enhanced dry matter translocation to the seed/grain. Among the P sources, commercial monoammonium phosphate (CMAP) and commercial triple superphosphate (CTSP) had similar effects on growth and yield, but different impacts on the nutrient concentrations of both crops, indicating the importance of selecting P source to improve crop quality. Zinc addition with reagent grade P decreased the concentrations of P, K, Ca, Mg and Cu in flax but not in durum wheat. We conclude that proper combination of P and Zn fertilizers is necessary to optimize crop yields, but that P had a proportionally greater effect in promoting yield in durum wheat than in flax. In contrast, Zn had a greater impact on mineral composition in flax than in durum wheat, which can affect the nutritional quality of the crop as a component of the human diet.