Iron (Fe) deficiency leads to an overproduction of reactive oxygen species (ROS) in plants that activate their antioxidant systems to control oxidative burst. In this study, contrasting Medicago truncatula genotypes, A17 and TN8.20 (tolerant) and TN1.11 (sensitive), were grown under Fe deficiency. The superoxide dismutase (SOD: EC1.15.1.1) activity, their isoforms’ coding genes, the copper chaperone expression patterns, and leaf phenolic contents were analysed. Our results showed that Fe deficiency decreases the photosynthetic capacity and plant biomass production with a prominent effect on TN1.11 genotype. The tolerance of A17 and TN8.20 was correlated with a maintenance of Fe content and the photosynthetic apparatus and an increase of Cu concentration compared with the sensitive genotype. We revealed a significant increase of H₂O₂ in Fe-deficient plants, mainly in TN1.11 sensitive genotype. TN8.20 and A17 tolerance were concomitant with a significant increase of SOD activities (SOD, Cu/Zn-SOD, and Mn-SOD) under Fe deficiency. This increment was correlated to an induction of the copper chaperone gene expression level, as well as an accumulation of isoquercitin phenolic compound. Our study provides new insights into the orchestration of SOD’s isoforms activities, the expression of the copper chaperone, FeSOD, Cu/ZnSOD genes, and the leaf phenolic compounds accumulation that allows Medicago truncatula to overcome Fe deficiency.