Selenium (Se) is an essential trace element for humans. Arbuscular mycorrhizal fungi (AMF) play a crucial role in increasing plant micronutrient acquisition. Soybean (Glycine max (Linn.) Merr.) is a staple food for most people around the world and a source of Se. Therefore, it is necessary to study the mechanism of Se intake in soybean under the influence of AMF. In this study, the effects of fertilization with selenite and inoculation with different AMF strains (Claroideoglomus etunicatum (Ce), Funneliformis mosseae (Fm)) on the accumulation and speciation of Se in common soybean plants were discussed. We carried out a pot experiment at the soil for 90 days to investigate the impact of fertilization with selenite and inoculation with Ce and Fm on the Se fractions in soil, soybean biomass, accumulation and speciation of Se in common soybean plants. The daily dietary intake of the Se (DDI) formula was used to estimate the risk threshold of human intake of Se from soybean seeds. The results showed that combined use of both AMF and Se fertilizer could boost total Se and organic Se amounts in soyabean seeds than that of single Se application and that it could increase the proportion of available Se in soil. Soybean inoculated with Fm and grown in soil fertilized with selenite had the highest organic Se. The results suggest that AMF inoculation could promote root growth, more soil water-soluble Se and higher Se uptake. The maximum Se intake of soybean for adults was 93.15 μg/d when treated with Se fertilizer and Fm, which satisfies the needs of Se intake recommended by the WHO. Combined use of AMF inoculation and Se fertilizer increases the bioavailable Se in soil and promotes the total Se concentration and organic Se accumulation in soybean. In conclusion, AMF inoculation combined with Se fertilization can be a promising strategy for Se biofortification in soybean.