This research explores the impact of elevated ozone (eO ₃), elevated carbon dioxide (eCO ₂), and their interaction on the yield and quality of mustard (Brassica juncea) crops through a Free Air Concentration Enrichment (FACE) experiment conducted in an open field setting. By examining a range of physiological parameters across different mustard varieties, this study aims to understand the responses of these crops to changing atmospheric conditions and identify genotypes with enhanced resilience to eO ₃ and adaptability to future eCO ₂ levels. Key physiological traits, including photosynthate availability, antioxidant and secondary metabolite production, and gas exchange parameters (photosynthetic rate, stomatal conductance, transpiration rate, and water-use efficiency), were analyzed at various growth stages to assess their correlation with yield and quality attributes under each treatment condition. The findings demonstrate that eO ₃ significantly reduces yield by impacting quaternary branches, seed yield, biomass, and other yield-related parameters, while eCO ₂ promotes yield and quality, enhancing photosynthesis and subsequent photosynthate accumulation. Notably, eCO ₂ was found to mitigate the adverse effects of eO3 on yield and fatty acid composition, indicating a potential buffer against ozone-induced stress. Among the studied varieties, Pusa Bold exhibited superior performance, showing particular resilience to eO3 and benefiting from eCO2 enhancement. Multivariate analysis and linear modeling of the physiological parameters highlighted significant treatment and genotypic differences, underscoring the complex interplay between environmental factors and crop physiology. The study’s outcomes suggest that selecting genotypes with tolerance to ozone and favorable responses to elevated CO2 could be pivotal in sustaining mustard production under future climatic conditions. This research contributes to the broader understanding of how elevated atmospheric gases influence agricultural crops, offering insights for breeding and management practices aimed at enhancing crop resilience and food security in the face of climate change.