The action-to-reaction dynamics of next-generation nanofertilizers (NFs) towards field crops are currently being addressed in precision and sustainable agriculture. Therefore, our aim was to evaluate the effects of foliar application of ZnO nanoparticles (ZnO-NPs) or their combination with hybrid nanoporous biosilica mixed with yeast (ZnSi-bio) for soybean plants' selected production and physiological indices in comparison to an NF-free control. The experiment was conducted at eco-friendly concentrations in Veľký Krtíš, Slovakia, a location within the Central European agronomical region. The ZnSi-bio variant had an improved number of pods, seed count, and yield, while the ZnO-NPs variant had an enhanced seed bulk density compared to the NF-free control, which had a greater effect on thousand-seed weight (TSW). Significant differences were found in the final quality components of soybeans with respect to phosphorus content without ZnO-NP biofortification. In the case of the ZnSi-bio variant, soybeans were biofortified with zinc. Both leaf-applied NFs markedly improved nutritional and energetic values for soybeans. NFs continued to positively affect seasonal physiology, such as the stomatal conductance (Ig) and crop water stress index (CWSI), compared to the control. The results suggest that the ZnO-NPs, especially when combined with hybrid biosilica and yeast, open new avenues for interdisciplinary research in agro-food science.