The aim of the study was to determine the effect of application of small amounts of nitrogen to the soil together with foliar application of micronutrients on the content of copper, manganese and zinc in the grain of spelt (Triticum aestivum ssp. spelta L.). The study was based on a two-factor field experiment conducted in 2009–2011 on very good rye complex soil. Nitrogen was applied in the form of ammonium nitrate (34% N), and manganese and copper were applied to the leaves in the form of the fertilisers Adob Mn (1.5 l∙ha−1) and Adob Cu (1.0 l∙ha−1), respectively. The results indicated that the nitrogen fertilisation, the foliar application of micronutrients and the interaction of these factors significantly determined the contents of copper, manganese and zinc in the grain. The highest content of Cu and Mn in the material was obtained following the application of 50 kg N·ha−1, and an increase in nitrogen application (to 50 kg·ha−1) caused a decrease in the content of zinc in the grain. Foliar application of Cu, Mn and both elements together resulted in significant changes in the concentrations of Cu, Mn and Zn in the plant material as compared to treatment without the application of micronutrients. The mineral fertilisers at the rates applied had a beneficial effect on the chemical composition of the grain, and thus on its quality, and this was achieved with substantially lower consumption of agrochemicals than that in the case of agrotechnical procedures for traditional cereals. It can, therefore, be concluded that this practice is environment friendly and can significantly reduce the negative impact of agricultural activity.