The nutritional quality of wheat is jeopardized by rising atmospheric carbon dioxide (CO₂) and the associated emergence and enhanced virulence of plant pathogens. To evaluate how disease resistance traits impact wheat nutritional content, 15 wheat cultivars with varying levels of resistance to Fusarium Head Blight (FHB) were grown at ambient and elevated CO₂. Although all wheat cultivars had increased yield when grown at elevated CO₂, on average the nutritional content of FHB moderately resistant (MR) cultivars was impacted more than susceptible cultivars. At elevated CO_2, the MR cultivars had more significant differences in plant growth and nutritional content. Furthermore, changes in protein, starch, phosphorus, and magnesium content were correlated with the cultivar FHB resistance rating, with more FHB moderately resistant cultivars having greater changes in nutrient content. This is the first report of a correlation between the degree of plant pathogen resistance and grain nutritional content loss in response to elevated CO₂. Our results demonstrate the importance of identifying wheat cultivars that can maintain nutritional integrity and FHB resistance in future atmospheric CO₂ conditions.