<p>Nanoparticles (NP) show promise as nutritional additives in agriculture, enhancing plant growth. In addition to protective and plant growth-supporting roles, their release to the environment, potential entry into the food chain, and toxicity pose significant challenges. This study aims to model a novel nano fertilizer to elucidate its uptake, transport, nutritional contribution, physiological effects, and potential genotoxicity on barley (<i>Hordeum vulgare</i> L.). A novel NP, MgAl₂O₄– magnesium aluminum oxide, was synthesized and characterized using field emission-scanning electron microscopy (FE-SEM), transmission electron microscopy (TEM), X-ray diffraction (XRD), and energy dispersive X-ray (EDX). A range of concentrations (50, 100, 200, and 400 mg L^− 1) were hydroponically applied and the seedlings’ physiological, morphological, and nutritional states were elucidated. The results showed that NP treatment (∼ 16.5&#xa0;nm) at 50 mg L^− 1 significantly improves plant growth indices, such as germination, leaf/root lengths, biomass, photosynthetic parameters, and relative water content (<i>P</i> &lt; 0.05). Compared with the control, the root length increased by 46% (50 mg L^− 1; <i>p</i> &lt; 0.01) and 30% (100 mg L^− 1; <i>p</i> &lt; 0.05). However, higher doses (≥ 200 mg L^− 1) led to a noticeable decrease in these indices. Moreover, adverse effects such as cell membrane injury, root morphology deformation, and genotoxicity were evident, leading to disruptions in ion and element trafficking. These findings underscore the need to carefully monitor nano fertilizer applications and determine their benefits as well as their potential toxic and genotoxic risks. This study contributes to our understanding of the environmental safety of engineered nano fertilizers.</p>