Selenium uptake and its content in soybean grains are affected by Se application methods. This study evaluated the impact of Se foliar application combined with a multi-nutrient fertilizer (MNF) on soybean, establishing a Se threshold to better understand the relationship between Se content in grains and yield of two genotypes (58I60 Lança and M5917). Two trials were conducted in a 4 × 2 factorial design: four Se rates (0, 10, 40, 80 g Se ha−1) and two methods of foliar Se application (Se combined or not with MNF). Foliar fertilizers were applied twice, at phenological stages of beginning of pod development and grain filling. Grain yield increased with the application of MNF, yet Se rates increased Se contents linearly up to 80 g Se ha−1, regardless of the use of MNF. Lança and M5917 genotypes had grain Se critical thresholds of 1.0 and 3.0 mg kg−1, respectively. The application of Se favored higher contents of K, P, and S in grains of genotype Lança and higher contents of Mn and Fe in grains of genotype M5917. Our findings highlight the importance of addressing different Se fertilization strategies as well as genotypic variations when assessing the effects of Se on soybean yield and grain quality.