Among the mineral elements required by humans, iron (Fe) is the most common cause of nutritional deficiencies, particularly anaemia. Legume plants are extremely important in the world's diet and they are major sources of mineral nutrients. However, when these plant foods are grown in calcareous soil, their production is severely affected by Fe deficiency chlorosis (IDC), and when less Fe is available for absorption, less amount of this element will be available for accumulation in the edible plant parts. As Fe plays critical roles in photosynthesis and respiration, when lacking this element, plants develop chlorosis and their growth is drastically reduced. IDC morphological symptoms were monitored in soybean (Glycine max), common bean (Phaseolus vulgaris) and the model crop barrel medic (Medicago truncatula). When compared to the other two legumes, G. max presented lower Fe-reduction rates and severe chlorosis, associated with lower SPAD values. Transcriptome analysis was performed in roots of the three species when grown in Fe deficiency and Fe sufficiency, and 114,723 annotated genes were obtained for all samples. Four IDC-related genes were up-regulated in common by the three species and can be considered key players involved in the IDC response, namely, metal ligands, transferases, zinc ion binding and metal ion binding genes. With regards to the genes most highly expressed under iron deficiency individually by each species, we found that the most highly expressed genes were a defensin in P. vulgaris, a phosphatase in M. truncatula and a zinc ion binding gene in G. max.