<p>Hydroxyapatite nanoparticles (HAP-NPs) have gained attention as a potential alternative to conventional fertilizers. However, recent studies reported their possible phytotoxic effects, necessitating evaluation of their biological impacts. In this study, HAP-NPs were synthesized using the wet chemical precipitation method and the successful synthesis was confirmed by various physico-chemical techniques. The effect of synthesized HAP-NPs was evaluated on 30-day-old faba bean (<i>Vicia faba</i> var. Saber 02) plants.&#xa0;Physiological analysis revealed that exposure of <i>V. faba</i> seedlings to HAP-NPs concentrations of 500 and 1000 mg L⁻¹ significantly (<i>p</i> &lt; 0.05) reduced shoot elongation and biomass accumulation. Cytotoxicity assessments in <i>V. faba</i> leaves indicated that HAP-NPs induced the generation of superoxide anion radicals (O₂^•−) and increased lipid peroxidation. Interestingly, electrolyte leakage (EL) decreased following HAP-NPs treatment. Concurrently, exposure to HAP-NPs markedly reduced membrane lipid content and altered fatty acid composition. Enzymatic assays showed that superoxide dismutase (SOD) activity was enhanced at both concentrations, whereas catalase activity (CAT) increased at 500 mg L⁻¹ but declined at 1000 mg L⁻¹ compared to control. Guaiacol peroxidase (GPX) activity remained unchanged at the lower dose but exhibited a slight increase at the higher concentration. Genotoxicity assays further revealed a significant reduction in the mitotic index (MI), accompanied by an elevated frequency of micronuclei (MN) and chromosomal anomalies (CA) in root meristematic tissue, particularly at the higher HAP-NPs concentration. These findings highlight the dose-dependent nature of HAP-NPs effects and underscore the importance of careful risk assessment to ensure their safe application in agriculture and environmental management.</p>