Reducing iron solubility in calcareous soils causes iron chlorosis symptoms in the plant. In order to investigate the response of M. scutellata to direct and indirect iron deficiency, a factorial experiment was conducted in a completely randomized design with three replications. The experimental factors included three levels of lime (0, 4 and 8%) and five levels of Fe (0, 5 and 10 mg Fe Kg soil-1 as soil application and 0 and 2.1 µM Fe as foliar spray). Zero Fe concentrations in soil and foliar Fe fertilization was considered as control-S and control-F treatment, respectively. The results showed that the amendment of 8% CaCO3 in control treatments caused typical Fe deficiency symptoms, including decreases in chlorophyll, total and extractable leaf Fe concentration, protein, leaf relative water content, membrane stability index and increases in leaf total phenolic and flavonoid concentration when compared to 0% lime. The soil and foliar Fe fertilisation led to the improvement of Fe chlorosis, increases in chlorophyll, Fe, protein, and decreases in concentration of phenolic compounds in three levels of lime. The foliar Fe fertilization in three levels of lime increased total and extractable leaf Fe content, compared to two soil Fe treatments, but foliar Fe fertilization (in 4 and 8% of lime) yielded progressively lower leaf phenolic compounds. The highest leaf chl concentration in 8% lime was observed in 10 mg Fe Kg soil-1 and foliar Fe fertilization. The presented data indicate that the use of foliar application of Fe (Fe- EDDHA) is potent to reduce the effects of lime induced chlorosis in plants in calcareous soils.