For many years, deficiencies in selenium (Se) and, sometimes, sulphur (S) have been observed in populations in most European countries and other parts of the world. This study aimed to determine the effect of selenium (0, 10 and 20 g Se ha−1) and the date of its application (in the tillering phase—BBCH 22–24 and in the stem elongation phase—BBCH 31–34) and sulphur application (0, 15 and 30 kg S ha−1) on the content of various forms of nitrogen (total nitrogen, protein nitrogen, ammonium nitrogen, and nitrate nitrogen) in winter spelt wheat and winter common wheat. Selenium application influenced nitrogen distribution in wheat. In spelt, grain total-N decreased by 4%, while common wheat straw increased by 13%. Application timing had no significant effect on total-N. Sulphur slightly raised total-N in common wheat grain and straw. Selenium reduced protein-N in spelt grain by 7% but increased it in common wheat straw by 18%. Ammonium-N in straw rose by 24–27%, while nitrate-N declined in grain and straw of both species. Sulphur-enhanced mineral N forms (ammonium-N by 6–16%, nitrate-N by 7–24%), especially in the early stages. Se–S fertilization strategies should consider their competitive uptake and impact on N metabolism.