Since plant’s edible parts are one of the most important sources of nutrition, agronomic biofortification plays a huge role in overcoming mineral deficiency worldwide. The field-based research trial was set up in 2 years (2020 and 2021) with seven different treatments of foliar Zn and Se biofortification: 1. control (without Se or Zn solutions); 2. Se_1 treatment: 10 g/ha Se; 3. Se_2 treatment: 20 g/ha Se; 4. Se_3 treatment: 30 g/ha Se; 5. Zn_1 treatment: 3 kg/ha Zn; 6. Zn_2 treatment: 6 kg/ha Zn; 7. Se_3 Zn_2 treatment: 30 g/ha Se + 6 kg ha Zn. There were six soybean varieties of the 00 to I maturity group (Ika, Korana, Lucija, Sonja, Sunce, and Toma) included in the study, which originated from the Agricultural Institute Osijek, Croatia. After sampling the plants at the harvest, the macro- and micronutrient status in the grain, pods, leaves, and stems were determined, as well as nutrient removal by the plant. In general, biofortification treatment has a very significant influence (p < 0.001) on both Zn and Se accumulation in soybean grain and the removal of the elements within all above-ground organs. The highest increments of Zn in the soybean grain were determined at the Zn_2 treatment, which was 43% higher than the control treatment. The Toma variety accumulates the highest Zn in the grain (61.47 mg/kg), and the Lucija variety accumulates the highest Se (1070.71 µg/kg). The Se content in the soybean grain was the highest at the Se_3 treatment, where it was 53 times higher compared to the control. The linear regression showed that for each kg Zn and g Se applied, the grain status increased by 3.18 mg/kg and 338.71 µg/kg, respectively. The highest Zn nutrient use efficiency (NUE) of foliar biofortification for grain (2.6%) and vegetative mass (4.4%) was with 3 kg/ha (Zn_1). Generally, for all the Se treatments, it was found that the seed and vegetative mass yields of 4.0 t/ha have average Se NUE, around 38%, and vegetative mass of around 6%.