<p>Climate change is considered as one of the most important environmental issues, which is posing a threat to the food and nutritional security of the world. Rising concentration of atmospheric carbon dioxide (CO₂) is a globally consistent and important contributor to climate change. Crops are sensitive to future climate changes and show variable responses to rising atmospheric CO₂. It is necessary to evaluate response of crops to elevated CO₂ to understand the adaptive capabilities of plants to climate change for formulation of strategies towards sustainable agriculture and development of climate-resilient crops in the future. The present study is the first to explore effects of high CO₂ on seed composition of mustard grown under realistic field conditions in Free Air CO₂ Enrichment Facility (FACE). Also, it is the first to report impact of elevated CO₂ on glucosinolates and ultrastructure of seeds of <i>B. juncea</i>. In this study, mustard plants (<i>Brassica juncea</i>) were grown under ambient CO₂ (390 µmol mol^-1), or elevated CO₂ (550 µmol mol^-1) in FACE. Elevated CO₂ significantly increased the concentration of total soluble sugars, oil content and C:N ratio in seeds. The study reports, for the first time, a statistically significant decrease in concentration of nitrogenous compounds such as aliphatic glucosinolates and their precursor, methionine, in seeds of <i>B. juncea</i> grown in FACE facility. Transmission Electron Microscopy (TEM) further revealed reduction in protein bodies in cotyledonary cell of mustard seeds at high CO₂. The findings of the study suggest that an increase in atmospheric CO₂ will significantly affect the nutritional quality, medicinal properties, and defense ability of the oilseed. Such changes are likely to affect global oilseed trade, commerce, and supply chains dependent on this crop. Therefore, this study highlights the need to develop climate-resilient mustard crop to ensure the maintenance of nutritional quality in its seeds under future climate change scenarios.</p>