Legumes, due to their symbiosis with papillary bacteria, can receive nitrogen from the air. The remaining nutrients must be supplied in fertilisers, either soil or foliar. In the pot experiment, we recorded the responses of two soybean cultivars (Annushka, Pompei) to the foliar application of micronutrients (control, Zn, Fe, Cu, Mn, B, or Mo). The physiological properties were expressed as net photosynthetic rate (PN), intercellular CO2 concentration (Ci), transpiration rate (E), stomatal conductance (gs), maximum quantum yield of photosystem II (Fv/Fm), maximum quantum yield of primary photochemistry (Fv/F0), photosynthetic performance index (PI), and the development of soil plant analyses (SPAD), which were analysed. The effects of individual micronutrients on nodulation, plant growth, and condition were also investigated. Micronutrient fertilisation had a positive effect on plant fresh weight and no negative effect on plant condition. It was shown that elements such as B, Fe, and Mo had the most beneficial effect on nodulation compared to the control, regardless of the cultivar analysed. The application of single-component foliar fertilisers improved the physiological parameters of the plants. The relative chlorophyll content was most favourably affected by the application of Mn, B, and Mo in the Annushka cultivar, and Fe, Mn, and Mo in the Pompei cultivar. Similarly, in the case of chlorophyll fluorescence, the most stimulating effect was found for Mn and B, regardless of the cultivar. In the case of gas exchange, the application of Fe, Mo, and B for the Annushka cultivar and Cu for the Pompei cultivar had the most favourable effect on physiological measurements. The results obtained indicate that the foliar application of the evaluated micronutrients is justified in soybean cultivation and does not disturb the nodulation process.