The study aimed to analyze the effects of extracts made from buckwheat grain, hulls, and bee products (propolis, bread, and pollen) and extraction solvents on the growth of microfungi on a medium and on buckwheat, wheat, oat, and maize grain. Research findings suggest that bioactive compounds contained in buckwheat grain reduced the amount of Fusarium spp. in the grain kept in the antifungal extract for 90 min at 25°C temperature. Buckwheat hull extract was more effective in inhibiting mycelial growth of mycotoxin‐producing Fusarium culmorum and Fusarium graminearum compared with buckwheat grain extract (13%–50% and 14%–36%, respectively). The antifungal activity of extracts of bee products did not depend on the content of phenolic compounds in them; however, it depended on the grain species treated. After treatment of oat, wheat, and maize grain with bee product extracts, the lowest concentration of microfungi was identified on oat grain. More significant analysis results were obtained for the samples where ethanol solvent had been used for the preparation of extracts. This paper focusses on the application of natural products for the protection of food raw materials against microfungal contamination. It is not possible to completely prevent grain contamination, because the reduction of the amount of predominant microfungi on grain creates conditions for the reproduction of propagules of other fungi. It is very important that the antifungal activity of bioactive compounds should be targeted at mycotoxin‐producing genera and species of fungi.