Chromium (Cr) is among the most widespread toxic trace elements found in agricultural soils due to various anthropogenic activities. However, the role of micronutrient-amino chelates on reducing Cr toxicity in crop plants was recently introduced. In the current experiment, the exogenous application of micronutrients [iron (Fe)] chelated with amino acid [lysine (lys)] was examined, using an in vivo approach that involved plant growth and biomass, photosynthetic pigments and gaseous exchange parameters, oxidative stress indicators and antioxidant response. The uptake and accumulation of Fe and Cr were determined under different levels of tannery wastewater (33, 66, 100%) used along with the exogenous supplementation of Fe-lys (5 mM) to Spinacia oleracea plants. Results revealed that tannery wastewater in the soil decreased plant growth and growth-related attributes, photosynthetic apparatus and Fe contents in different parts of the plants. In contrast, the addition of different levels of tannery wastewater to the soil significantly increased the contents of malondialdehyde (MDA), hydrogen peroxide (H2O2) and electrolyte leakage (EL), which induced oxidative damage in the roots and leaves of S. oleracea plants. However, S. oleracea plants increased the activities of superoxide dismutase (SOD), peroxidase (POD), catalase (CAT) and ascorbate peroxidase (APX), which scavenge the over-production of reactive oxygen species (ROS). Cr toxicity can be overcome by the supplementation of Fe-lys, which significantly increased plant growth and biomass, improved photosynthetic machinery and increased the activities of different antioxidative enzymes, even in the plants grown under different levels of tannery wastewater in the soil. Furthermore, the supplementation of Fe-lys increased the contents of essential nutrients (Fe) and decreased the contents of Cr in all plant parts compared to the plants cultivated in tannery wastewater without application of Fe-lys. In conclusion, the application of Fe-lys is an innovative approach to mitigate Cr stress in spinach plants, which not only increased plant growth and biomass but also decreased the Cr contents in different plant organs.