Ozone (O3) is an oxidative pollutant that significantly threatens plant development and ecological dynamics. The present study explores the impact of O3 on Moringa (Moringa oleifera) ecotypes when exposed to ambient and elevated O3 levels. Elevated O3 concentrations resulted in significant reductions in total biomass for all ecotypes. Photosynthetic parameters, including stomatal conductance (gsto), CO2 assimilation (Pn), and carboxylation efficiency (K), decreased under elevated O3 in some ecotypes, indicating a detrimental effect on carbon assimilation. Nonstructural carbohydrate (NSC) levels in roots varied among ecotypes, with significant reductions in starch content observed under elevated O3, suggesting a potential shift towards soluble sugar accumulation and reallocation for antioxidant defense. Secondary metabolite analysis revealed increased polyphenol production, particularly quercetin derivatives, under elevated O3 in specific ecotypes, highlighting their role in mitigating oxidative stress. Interestingly, the glucosinolate content also varied, with some ecotypes exhibiting increased levels, suggesting a complex regulatory mechanism in response to O3 exposure. The study underscores the intrinsic variability among Moringa ecotypes in response to O3 stress, emphasizing the importance of genetic diversity for adaptation. The findings indicate that Moringa's metabolic plasticity, including shifts in NSC and SM production, plays a crucial role in its defense mechanisms against O3-induced oxidative stress. These insights are vital for optimizing the cultivation and utilization of Moringa in diverse environmental conditions, particularly in regions with elevated O3 levels.