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With the growing demand for products fortified with biologically active substances, consumer interest in whole-grain products is also growing. Whole grains are rich in fiber, vitamins, minerals, and antioxidants. However, biotechnological solutions are required to increase the nutritional value of grain products, including the use of enzyme preparations such as carboxylases and phytases. The purpose of this study was to study the effect of a complex enzyme preparation containing cellobiohydrolase, xylanase, beta-glucanase, and phytase on changes in the microstructure of the wheat grain surface and the aleurone layer, trace element, carbohydrate composition, fatty acid profile, and antioxidant activity. The study's objects were whole grains and the aleurone layer of Moskovskaya 39 wheat. After fermentation, cross sections of the grain surface and the aleurone layer were examined using a scanning electron microscope. The study of the aleurone layer revealed incorrect packaging of protein balls and fuzzy boundaries. It was shown that the content of phosphorus, sulfur, calcium, and copper in the grain after fermentation was significantly lower than in the native grain, by an average of 1.5 – 2 times. The rate of phosphoric acid release from wheat grain treated with the enzyme preparation was higher than under the action of the endogenous phytase of the grain when soaked in water. The total sugar content in grains soaked in the enzyme solution increased significantly by 22.22% (p <0.05) compared to native grains. After soaking, the levels of unsaturated fatty acids in wheat increased, including linoleic acid, α-linolenic acid, γ-linolenic acid, and erucic acid. At the same time, the content of oleic acid decreased. The increase in unsaturated fatty acid content is probably due to their synthesis during the grain swelling period. The antioxidant activity of grain soaked in an enzyme preparation solution was significantly (p <0.001) higher than that of native grain and grain soaked in water by 3.0 and 1.6 times, respectively. Thus, the experimental data indicate that treating wheat grain with a complex enzyme preparation containing carboxyhydrazes and phytase is an effective means of increasing the grain's nutritional value.