The comparative study on the effects of nitrapyrin and the mixture of natural siliceous minerals on physiological processes of some economically important crops with different pathways of carbon fixation grown under high nitrogen fertilization conditions, as well as on soil microbiota and the content of macronutrients was conducted in the 5-years field experiments. The results obtained revealed a significantly higher inhibitory effect of siliceous minerals on the supply of nitrate forms of nitrogen to corn and winter wheat grown on different types of soils, amended with urea (60-100 kg / ha) during the whole period of the study. Microbiological analysis showed that application of siliceous minerals significantly decreased the number of nitrifiers as well as the number of micromicetes producing phytotoxic allelochemicals compared with the other treatments. The concentration of phytotoxic phenolics was also lower in soil amended with the siliceous minerals as compared to the other plots. The application of nitrapyrin significantly reduced the concentration of chlorophyll b and carotenoids, but slightly increased the content of chlorophyll a in the leaves of wheat and corn plants. While application of siliceous minerals stimulated accumulation of chlorophyll b in the leaves of the both crops indicating intensification of growth processes. Application of nitrapyrin led to the reduction in the content of aspartate and some aromatic amino acids, but stimulated the accumulation of arginine and lysine. Such metabolic changes suggested disintegration of nitrogen and phosphate metabolism in the studied crops. Crops treated with siliceous minerals had higher glutamic acid concentration, which indicated the intensification photosynthetic processes. Thus, the use of natural siliceous minerals is more advantageous than traditional nitrification inhibitors such as nitrapyrin in terms of their effectiveness, persistence in various types of soils and beneficial effect on soil microbiota. Their production is cheaper and harmless to the environment.