Engineered nanomaterials are increasingly used in everyday life applications and, in consequence, significant amounts are being released into the environment. From soil, water, and air they can reach the organelles of edible plants, potentially impacting the food chain and human health. The potential environmental and health impact of these nanoscale materials is of public concern. TiO₂ and ZnO are among the most significant nanomaterials in terms of production amounts. Our study aimed at evaluating the effects of large-scale TiO₂ (~100 nm) and ZnO (~200 nm) nanoparticles on soybean plants grown in vitro. The effect of different concentrations of nanoparticles (10, 100, 1000 mg/L) was evaluated regarding plant morphology and metabolic changes. ZnO nanoparticles showed higher toxicity compared to TiO₂ in the experimental set-up. Overall, elevated levels of chlorophylls and proteins were observed, as well as increased concentrations of ascorbic and dehydroascorbic acids. Also, the decreasing stomatal conductance to water vapor and net CO₂ assimilation rate show higher plant stress levels. In addition, ZnO nanoparticle treatments severely affected plant growth, while TEM analysis revealed ultrastructural changes in chloroplasts and rupture of leaf cell walls. By combining ICP-OES and TEM results, we were able to show that the nanoparticles were metabolized, and their internalization in the soybean plant tissues occurred in ionic forms. This behavior most likely is the main driving force of nanoparticle toxicity.