Aims <p>Symbiotic nitrogen fixation (SNF) has the potential to enhance the yield of legume crops, particularly under low nitrogen conditions. Selenium (Se) has been demonstrated to enhance plant adaptability to the environment. In this study, the effects of selenite on the growth of soybean and SNF were investigated.</p> Methods <p>A hydroponics experiment with four selenite concentrations (0, 0.5, 2, and 10 μM) and a soil experiment with three selenite application rates (0, 2, 5 mg kg⁻¹) were carried out. The soybean variety Zhonghuang 13 and <i>Bradyrhizobium diazoefficiens</i> USDA110 were utilized as experimental materials, Na₂SeO₃ used as the Se source.</p> Results <p>The application of Se significantly promoted soybean growth and improved physiological performance. Nodule biomass increased by 36.79% and 32.65% under 10 μM and 5 mg kg⁻¹ Se treatments, respectively, compared to the CK. Nitrogenase activity was markedly improved by 313% under 10 μM Se in hydroponic conditions. Se also elevated nitrogen content in soybean plants, promoting carbohydrate accumulation and transport. The activities of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) in leaves increased, whereas the malondialdehyde (MDA) content decreased in both roots and leaves following Se application. Metabolomics analysis revealed that Se treatment upregulated amino acid metabolism and the citrate cycle pathways in soybean roots, while downregulating the biosynthesis pathways of flavones, isoflavonoids, and flavonoids.</p> Conclusions <p>Selenite promotes soybean and nodule growth while enhancing SNF efficiency. Our results provide a theoretical basis for improving legume production by using Se fertilizer in the context of low nitrogen inputs.</p> Graphical Abstract <p></p>