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Co-inoculation of soybeans with <i>Bradyrhizobium</i> and plant growth-promoting bacteria has displayed promise for enhancing plant growth, but concrete evidence of its impact on soybean yields is limited. Therefore, this study assessed the comparative efficacy of two 1-aminocyclopropane-1-carboxylate deaminase-producing <i>Pseudomonas</i> species (OFT2 and OFT5) co-inoculated with <i>Bradyrhizobium ottawaense</i> (SG09) on the growth, physiology, nodulation efficiency, and grain yield of three major Japanese soybean cultivars: Enrei, Fukuyutaka, and Satonohohoemi. The experiments were conducted in a warehouse under natural light conditions. The treatments included the inoculation of SG09, SG09 + OFT2, and SG09 + OFT5. Compared with <i>Bradyrhizobium</i> inoculation alone, co-inoculation led to significant improvements in nodulation efficiency, growth, and physiological performance in the Enrei and Fukuyutaka cultivars, but not in the Satonohohoemi cultivar. Furthermore, co-inoculation significantly boosted the total nitrogen content and ion uptake in the shoots, ultimately leading to a remarkable improvement in the grain yield in the Enrei and Fukuyutaka cultivars. These findings contribute to clarifying the interplay among <i>Bradyrhizobium</i>, <i>Pseudomonas</i>, and the plant host cultivar. Notably, <i>Bradyrhizobium</i>–<i>Pseudomonas</i> co-inoculation represents a potentially effective biofertilization strategy for soybean production, highlighting promising avenues for sustainable agricultural practices.