The exposure of the seeds to environmental stresses constitutes a limiting factor that controls the success of germination and the creation of new seedlings. Germination rate and seedling growth from bean were examined after imbibition of seeds with deionized water (control), co-precipitation Fe3O4 NPs1 (43 nm), or green synthesis Fe3O4 NPs2 (6 nm). Fe3O4 NPs increased the germination rate. The results showed that Fe3O4 NPs2 had a higher positive effect on seed germination and growth compared to Fe3O4 NPs1. The effects of Fe3O4 NPs1 and Fe3O4 NPs2 on the germination of bean seeds varied depending on NP concentrations and sizes. Fe3O4 NPs2 caused higher metabolic activities (increase in amino acids and soluble sugar contents) and lower solute leakage, which controlled seed viability. Moreover, peroxidase (GPOX; EC 1.11.1.7) and dehydrogenase (EC; 1.1.1.1) activities were induced in response to NPs application, which improved defense mechanisms and reduced oxidative damage. Fe3O4 NPs2 had a greater favorable effect on seed germination and growth than Fe3O4 NPs1. Following nanoparticle dose control for each plant species, we advise using green synthesis NPS in the new agricultural products.