To mitigate the adverse effects of nutrient stress under elevated atmospheric [CO2] on grain mineral composition and cooking quality, selection of crop varieties that are productive and maintain grain nutritional quality is important. Rice (Oryza sativa L.) varieties, IR64-Pup1.1, IR64, and Kasalath, were grown in open top chambers (OTC) with elevated [CO2] (700 ± 50 ppm), OTC with ambient [CO2], and open control-ambient [CO2] with two levels of phosphorus (P), low (7.96 mg P kg−1 soil) and sufficient (22.9 mg P kg−1 soil) to study the interactive effects of P and [CO2] on grain quality. Grain quality traits varied significantly among varieties under elevated [CO2] but P nutrition effect was not significant. The concentration of N reduced significantly but P, K, Mg, and Ca increased under elevated [CO2] compared to open control-ambient [CO2]. Micronutrients Cu, Mn, Ni, and Zn increased significantly except Fe, while Al increased by > 50% under elevated [CO2] compared to open control-ambient [CO2]. Free sugars (glucose, fructose, and maltose) increased 3 to 5-folds but protein decreased significantly as C:N ratio altered at elevated [CO2]. Among cooking qualities, elevated [CO2] increased amylose and gel consistency resulting in increased viscosity of cold paste gel of cooked rice and boiling time of rice grain. Grain dimension was not affected by elevated [CO2] or P level. Among varieties, IR64-Pup1.1 performed better under elevated [CO2] irrespective of P levels as compared to Kasalath and IR64. Ours is the first report on grain quality assessment of IR64-Pup1.1 under elevated [CO2] and low P availability.