In order for a strain to be considered a probiotic or suitable plant bioprotective agent, it must have proven antimicrobial activity against pathogenic bacteria and phytopathogenic fungi. Bacillus amyloliquefaciens M exhibited significantly high antifungal activity against pathogenic fungi of the genera Aspergillus, Penicillium, Fusarium, and Sclerotinia; yeasts of the genera Candida and Saccharomyces; as well as high antibacterial activity against pathogens of the genera Escherichia, Salmonella, Staphylococcus, Listeria, Pseudomonas, and Bacillus. The manifested antimicrobial activity was influenced by the composition of the growth medium. The antifungal activity of the strain was investigated at growth temperatures of 30 °C and 37 °C, and at different pH values in aerobic and anaerobic cultivation, under static and dynamic culturing conditions. High antifungal activity was observed at the 24th h on both growth media (LBG broth and MPB broth) at pH = 6 and pH = 7 in aerobic and anaerobic cultivation. Bacillus amyloliquefaciens M produced antibiotic substances at pH > 5.0, and the antibiotic substances were either secreted into the medium or associated with the cell surface. Four compounds with different antifungal activity and different Rf values were registered through thin-layer chromatography (Rf1 = 0.47; Rf2 = 0.55; Rf3 = 0.67; and Rf4 = 0.75), two of the compounds were ninhydrin-positive. Bacillus amyloliquefaciens M was cultured in a bioreactor with stirring, and the parameters of the growth kinetics and the sporulation kinetics have been modeled. A spore concentrate of Bacillus amyloliquefaciens M has been obtained. In further research, the efficiency of the concentrate as a plant bioactive agent will be tested.