The production of safe and high quality food in a way that protects the natural environment is now associated with the use of biostimulants in agricultural crops. In practice, it is difficult to ensure effective protection of plants against various types of abiotic factors. In addition, modern agriculture strives to reduce the use of mineral fertilizers and chemical plant protection products for natural products. In soya cultivation, bacterial and fungal pathogens are extremely dangerous, their occurrence depends not only on weather conditions, resistance of varieties but also on some agrotechnical treatments. Therefore, regulators of plant growth and development may respond to the challenges and problems in soybeans cultivation. In the available literature, there is few information on the impact of the use of regulators of plant growth and development on the microbiological state of seeds. Therefore, the aim of this study was to investigate the influence of a natural biostimulant, based on the extract from seaweed and free amino acids, on the colonization of soybeans by microorganisms. The microbiological quality of seeds is extremely important for their industrial use. The article also presents the results of identification of dominant bacteria and fungi occurring on the soybean seeds Glycine max (L.) Merr. Field experiments were conducted in the years 2014-2016. During the growing season a biostimulant based on the extract of brown algae (Ascophyllum nodosum) and amino acids of plant origin (alanine, glycine, serine, valine, arginine, cysteine, hydroxyproline, lysine, methionine, phenylalanine, tyrosine, proline, threonine, and others) was used. The biostimulant was used in four combinations: single spraying at a concentration of 0.1% and 0.2% in the phase BBCH 13-15 and twice spraying in phases BBCH 13-15 and BBCH 61 and the obtained results were compared with a control combination in which to spray plants only water was used. The conducted research proved that the application of a natural biostimulant reduced the number of microorganisms on soybeans. It was found that the number of bacteria and fungi colonizing soybeans was reduced compared to the control depending on the number of applications and the concentration of biostimulant used in the cultivation. In microbial seeding, bacteria predominated - 86%, while only 14% were fungi. Among the identified bacteria, the dominant type was Bacillus, among the fungi Aspergillus sp. and Penicillium ssp. The results obtained from the conducted research, the biostimulant application limited the number of microorganisms. In connection with the above, the conclusion is that thorough observation of plants and knowledge of microorganisms that inhabit them allowed for early response and protection of plants through the use of, among others, biostimulants.