An assessment is made of the effect of spraying plants with biological products on the total microbiome of seeds of a new crop. The studies were carried out on three varieties of spring wheat of domestic breeding - Yoldyz, Burlak and Ulyanovsk-105. Preparations based on strains of endophytic bacteria isolated from seeds of spring wheat (Bacillus mojavensis PS17, Bacillus velezensis KS25) and spring barley (Bacillus velezensis KS31, Bacillus subtilis KS38) were used as biological preparations. The treatment of spring wheat crops was carried out in the phase of entry into the tube using the biological product consumption rate of 1.0 l/ha. The impact of treatments on the fungal and bacterial microbiome was assessed using quantitative PCR methods with the determination of the total (total) DNA of microorganisms per unit weight of seeds. In most cases, the use of treatment with endophytic bacteria reduces the amount of total micromycete DNA on seeds. Among the studied isolates, the Bacillus subtilis KS-38 strain was especially distinguished, which provided a significant (7.7-11.1 times) decrease in this indicator in all varieties. Bacillus mojavensis PS-17 had a significant effect (a decrease of almost 47 times) on the Ulyanovska 105 variety, and Bacillus velezensis KS-31 on the Burlak variety. On varieties Yoldyz and Ulyanovska 105, the most significant decrease in the total DNA of micromycetes was noted for endophytes obtained from spring wheat seeds (Bacillus mojavensis PS-17, Bacillus velezensis KS-25), and on variety Burlak, endophytes from spring barley seeds (Bacillus velezensis KS-31 and Bacillus subtilis KS-38). The decrease in the total DNA of micromycetes in the experiments was due to the use of the studied biological products and, to a lesser extent, varietal characteristics. For the bacterial microbiome, there were strong differences between varieties. A significant increase in the total DNA of bacteria in all studied varieties was in Bacillus mojavensis PS-17 and Bacillus velezensis KS-31. The variety (29.9%) made the greatest contribution to the variability in the content of total bacterial DNA in seeds, and the contribution of biological preparations was lower (25.5%). In the experiments, no correlation was found between the indicators of the total DNA of micromycetes and bacteria in spring wheat seeds.