The spread of antibiotic resistance and mineral depletion in soils encourages an intensive search for highly effective and environmentally safe bactericidal agents and sources of macro- and micro-elements. The most profitable solution would combine both the described tasks. Ultrafine particles (UFPs) have this functionality. Thus, this study aimed to analyze the bioluminescence and external morphological changes of Escherichia coli cells after contact with M2O3 and Co3O4 UFPs at effective concentrations (ECs). The antibiotic properties of the studied samples were determined on a multifunctional microplate analyzer TECAN Infinite F200 (Tecan Austria GmbH, Austria) by fixing the luminescence value of the bacterial strain E. coli K12 TG11 (Ecolum, NVO Immunotech Closed Joint Stock Company, Russia). Morphological changes in the cell structure were evaluated using a Certus Standard EG-5000 atomic force microscope equipped with NSPEC software (Nano Scan Technology LLC, Russia). The obtained results indicate high bactericidal properties of Co3O4 and Mn2O3 UFPs (EC50 at 3.1 × 10-5 and 1.9 × 10-3 mol/L, respectively) due to the degradation of the cell wall, pathological increase in size, disruption of septic processes, and loss of cytoplasmic contents. The prospects for the environmentally safe use of ultrafine materials are outlined. The limits of the dosages of Co3O4 and Mn2O3 UFPs recommended for further study in vitro and in vivo in feeding farm animals are established (no more than 4.9 × 10-4 mol/L for Mn2O3 UFPs and 1.5 × 10-5 mol/L for Co3O4 UFPs). The limitation of the work is the lack of experiments to determine the mechanisms of the toxic effect of UFP on bacteria, protein structures, and DNA and oxidative stress, which is planned to be performed in the future together with in situ and in vivo studies on animals.