ABSTRACT Application of iron nanoparticles as iron fertilizer can be a functional strategy to manage iron deficiency in agricultural crops. However, the toxicity of iron should not be ignored and its proper concentrations should be determined. The effect of iron nanoparticles and Fe (II) ethylenediaminetetraacetate (FeEDTA) on iron accumulation, photosynthetic pigments, soluble carbohydrate and protein, antioxidant enzymes activity, and lignification were compared in vitro in Solanum villosum. Culture media were prepared in two ways: 1) including 628 mg L−1 FeEDTA as control, and 2) different concentrations of iron oxide nanoparticles (628 and 730 mg L−1 in pH of 5.2, and 628 and 830 mg L−1 in pH of 5.9). Seeds were germinated on culture media and biochemical parameters were measured at the end of the fourth week. The iron content, amount of chlorophyll, soluble carbohydrate and protein in leaves and stems of the plants grown using the nanoparticle concentration of 628 mg L−1 decreased compared to the control, but the same parameters increased in concentrations of 730 and 830 mg L−1. Iron nanoparticles decreased catalase and ascorbate peroxidase activities. Guaiacol peroxidase activity and carotenoid content showed no significant difference between FeEDTA and nanoparticle treatments. Leaf and stem lignin levels did not differ from control (FeEDTA). FeEDTA can be replaced by optimum concentrations of iron nanoparticle under in vitro conditions. In vivo experiments are needed to generalize these results for field-grown plants, because iron nanoparticles have some advantage over iron chelate, which is highly dependent on soil conditions. Abbreviations: APX: ascorbate peroxidase; CAT: catalase; FeEDTA: Fe (II) ethylenediaminetetraacetate; GP: guaiacol peroxidase; MS: Murashige and Skoog medium