South African soils generally lack native Bradyrhizobium strains that nodulate and fix atmospheric nitrogen (N2) in soybeans (Glycine max L.). It is therefore very important to inoculate soybeans with products that contain effective Bradyrhizobium strains as active ingredients. In this study, a field experiment was conducted on two bioclimatic zones in South Africa during the 2019/2020 season to assess the effect of Bradyrhizobium japonicum strain WB74 inoculant formulation on nitrogen fixation, growth and yield improvement in soybeans. The first bioclimatic zone was characterized by a sandy clay loam soil, whereas the second bioclimatic zone has a sandy loam soil. The results showed that inoculation of soybeans with both peat and liquid formulations of Bradyrhizobium japonicum WB74 increased nitrogen uptake, which resulted in yield increase. The amount of N fixed was measured as 15N isotopes and increased with all treatments compared to the uninoculated control in both liquid and peat inoculant formulations. In bioclimatic zone A, slightly better results were obtained using the liquid formulation (1.79 t ha−1 for liquid compared to 1.75 t ha−1 for peat treatments), while peat formulations performed better in bioclimatic zone B (1.75 t ha−1 for peat compared to 1.71 t ha−1 for liquid treatments). In both areas higher yields were obtained with the formulations used in this study compared to the registered standards (treatment T3). The findings in this study provide vital information in the development and application of formulated microbial inoculants for sustainable agriculture in South Africa.