Zero valent iron nanoparticles (nZVI) attract interest given their effectiveness in soil remediation. However, little attention has been given to their impacts on plants. Likewise, although fertilizers are commonly used to enhance phytoremediation, their effects on As mobilization, resulting in potential toxic effects, require further study. In this context, we examined the impact of As and Hg accumulation on the antioxidative system of Medicago sativa grown in a soil amended with organic fertilizer and/or nZVI. The experiment consisted of 60 pots. Plants were pre-grown and transferred to pots, which were withdrawn along time for monitoring purposes. As and Hg were monitored in the soil-plant system, and parameters related to oxidative stress, photosynthetic pigments, and nonprotein thiol compounds (NPTs) were measured. In general, the application of nZVI immobilized As in soil and increased Hg accumulation in the plant, although it surprisingly decreased oxidative stress. Plants in nZVI-treated soil also showed an increase in NPT content in roots. In contrast, the application of the fertilizer mobilized As, thereby improving bioaccumulation factors. However, when combining fertilizer with nZVI, the As accumulation is mitigated. This observation reveals that simultaneous amendments are a promising approach for soil stabilization and the phytomanagement of As/Hg-polluted soils.