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The legume-rhizobium symbiosis plays an important role in the nitrogen (N) assimilation of plants, more particularly in the humid tropical region where soils are deeply weathered and have poor electrochemical properties. On acidic soils of Haut-Katanga, DR Congo it is not clear how application of Bradyrhizobium japonicum affect N allocation among soybean organs (e.g., leaves, seeds). Here, we assessed the effect of Bradyrhizobium japonicum on N content of soybean leaves and seeds cultivated on acidic soils. We conducted two experiments using a split-plot setup with three replicates in two sites (i.e., Kasapa and Kanyameshi). The main plots included three strains of Bradyrhizobium plus the uninoculated control and four varieties of soybean in the subplot. We found that the different strains of Bradyrhizobium did not induce significant effects on the total N content of soybean leaves and seeds in the Kasapa site. In contrast, Bradyrhizobium affected significantly the N content of soybean leaves in the Kanyameshi site. We demonstrated that N content in the soil, which varies between the two sites, positively influences yield and nodulation. We conclude that that the efficiency of the soybean-Bradyrhizobium symbiosis and its influence on the allocation of N through soybean plants strongly depend on the chemical characteristics of the soil and particularly on the initial levels of N in the soils.