Selenium (Se) biofortification during germination is an efficient method for producing Se-enriched soybean sprouts; however, few studies have investigated Se distribution in different germinated soybean proteins and its effects on protein fractions. Herein, we examined Se distribution and speciation in the dominant proteins 7S and 11S of raw soybean (RS), germinated soybean (GS), and germinated soybean with Se biofortification (GS-Se). The effects of germination and Se treatment on protein structure, functional properties, and antioxidant capacity were also determined. The Se concentration in GS-Se was 79.8-fold higher than that in GS. Selenomethionine and methylselenocysteine were the dominant Se species in GS-Se, accounting for 41.5–80.5 and 19.5–21.2% of the total Se with different concentrations of Se treatment, respectively. Se treatment had no significant effects on amino acids but decreased methionine in 11S. In addition, the α-helix contents decreased as the Se concentration increased; the other structures showed no significant changes. The Se treatment also had no significant effects on the water and oil-holding capacities in protein but increased the foaming capacity and emulsion activity index (EAI) of 7S, but only the EAI of 11S. The Se treatment also significantly increased the antioxidant capacity in 7S but not in 11S. This study indicates that the dominant proteins 7S and 11S have different Se enrichment abilities, and the protein structures, functional properties, and antioxidant capacity of GS can be altered by Se biofortification.