Abstract In this paper, the morphology of Escherichia coli bacteria grown in the presence of magnesium isotopes (magnetic 25 Mg, non-magnetic 24,26 Mg and natural Mg), and antibiotics of various groups were studied. Atomic force microscopy (AFM) was used as the main method. When the bacteria were cultured in the presence of different groups of antibiotics, the following morphological changes were detected: filamentation, cell lysis, cell adhesion, cell wall damage, and the formation of “depressions” or pores. For E. coli bacteria cultured on a medium with tobramycin and lincomycin, a magnetic magnesium isotope effect 25 Mg in bacteria morphology was detected, which was manifested as a change in the roughness of bacterial cells. Both of these antibacterial drugs act on the same intracellular system – protein synthesis. It has also been observed that the elongation of bacterial cells, when exposed to levofloxacin and ciprofloxacin, depends on the type of magnesium isotope in the nutrient medium. The combined action of the 25 Mg magnetic isotope and quinolones on bacteria makes it possible to obtain the process followed by significant elongation of cells, thereby indicating improved antibiotic effect, as compared with the nonmagnetic 24,26 Mg isotopes.