Significant advances have been achieved in the biofortification of common beans to increase bioavailable Zinc (Zn) and iron (Fe) but the mechanisms involved remain poorly understood. We explored relationships between phosphate (Pi) nutrition and Zn and Fe accumulation in four bean genotypes (Edar, Nizok, Colorado and Chimbolos) that nominally show differences in seed Fe and Zn accumulation. Edar seeds had the lowest phytic acid-to-iron molar ratios, which is a measure of iron bioavailability, under full nutrient conditions. Phosphate limitation impaired plant metabolism and yield, decreasing seed Pi and phytate levels but with no effect on seed Fe and Zn accumulation. Edar plants had a higher seed yield under low Pi than the other lines. Analysis of the seed proteome also revealed that Edgar was highly resistant to Pi deficiency. The phytic acid-to-iron molar ratios in Edgar seeds under Pi deficiency was about twice that of low phytic acid ( lpa) beans that have a 90% lower phytic acid content compared to conventional beans. Proteome analysis revealed that primary metabolism is shifted in the lpa beans, particularly regarding carbohydrate metabolism. We conclude that the ability to maintain Pi cycling and transport pathways is important in controlling seed phytic acid-to-iron molar ratios.