Elevated CO2 increases soybean growth and photosynthesis, and the resulting additional supply of photosynthates stimulates nodule activity. To characterize its biochemical response to both CO2 and bradyrhizobial strains, soybean inoculated with three strains of Bradyrhizobium japonicum was grown in growth chambers under ambient (400 µmol·mol–1) or elevated (800 µmol·mol–1) CO2. Soluble sugars were generally more abundant in leaves and nodules under elevated CO2, while starch and pinitol were depleted, indicating that additional photosynthates were rapidly used, in particular for nodule growth (dry mass increased by 65%). Ureides (allantoin and allantoic acid) increased under elevated CO2 in leaves, while this increase was not significant in nodules. The indigenous strain 12NS14 induced the highest ureides concentration in nodules under elevated CO2 along with the highest nitrogenase activity and increase in shoot dry mass, indicating a positive-feedback stimulation: soybean mobilized energy reserves to support more nodules, and in return nodules synthesized more ureides to support plant growth. In contrast, the commercial strain 532c resulted in the highest ureide concentrations in leaves, coupled with the lowest nitrogenase activity and nodules yield, suggesting a feedback inhibition of nodule activity. Our results show that selection of B. japonicum strains better adapted to elevated CO2 could improve soybean performance.