The paper demonstrates an antimicrobial effect of metabolite complexes of Lactobacillus rhamnosus GG and Saccharomyces boulardii, obtained by own method, after 6 months’ storage in a frozen state (−23 ± 1ºС) in respect of Staphylococcus aureus, Staphylococcus haemoliticus, Enterococcus faecalis, Corynebacterium xerosis with multidrug resistance. Increase in diameters of growth inhibition zones (by (3.0 ± 0.4)–(6.1 ± 0.3) mm) for all the investigated pathogens under the influence of metabolite complexes (freshly obtained and after storage) with azithromycin has been proven. No significant difference in antimicrobial activity of antibacterial agents with freshly obtained complexes and after storage at (−23 ± 1)°C was found. The expediency of using the chosen storage method to design the brand new products as well as development of ‘auxiliary drugs’ for antibiotics was confirmed.