Wheat is one of the most widely cultivated cereal crops in Poland and constitutes an important source of human nutrition. Therefore, the biofortification of wheat with selenium offers an opportunity to increase the intake of this nutrient in both human and animal diets. The aim of the study was to evaluate the effects of different sulphur and selenium doses, as well as the timing of their application, on the copper and zinc contents in wheat grain and straw. The experiment was conducted on Luvisol (silt loam), classified according to PTG (2019) and WRB (2022) systems. Three experimental factors were considered in the study. The first factor was the sulphur dose, applied at three levels (S0, SI, SII), and the second was the selenium dose, also applied at three levels (Se0, SeI, SeII). The third factor was the timing of selenium application, tested at two stages: tillering (BBCH 22–24) and stem elongation (BBCH 31–34). The field trials included 108 experimental plots, each measuring 3 × 6 m (18 m²). The test plants were winter spelt wheat (Triticum spelta L.) cv. Rokosz and winter common wheat (Triticum aestivum L.) cv. Astoria. The results demonstrated a beneficial effect of selenium application on zinc content in both spelt and common wheat grains. At lower doses, selenium may have increased the copper content in spelt wheat straw; however, overall, it reduced the copper content in common wheat grain. Sulphur fertilization increased the copper content in the grains of both wheat species, decreased the zinc content in common wheat grain, and increased the zinc content in the straw of both species.