Essential oils (EOs) extracted from Thymus vulgaris L. (TEO) and Rosmarinus officinalis L. (REO) have aroused interest in their application to food preservation or in alternative medicine or aroma-therapy. In this study, the chemical compositions of essential oils were determined and analyzed. The purpose of the investigation was to investigate in detail the activity of essential oils extracted from herbs (thyme and rosemary) and exposed to rotating magnetic filed (RMF) against the model Gram-negative bacteria Escherichia coli The bacterial removal has been optimized by a surface response methodology (RSM). It was shown that TEO in a concentration of 10 µL/50 mL of water resulted in a total bacterial number reduction after 40 min under the RMF. Rosemary's antibacterial effect was much weaker. Thus, we summarized that the rotating magnetic fields at a frequency of 27 Hz can increase the antimicrobial efficiency but the effect depends on the type of essential oil. High-rate bacteria removal was obtain for thyme oil in concentration of 30 µL of thyme oil to 50 mL of bacterial suspension, exposed to RMF at a frequency of 27 Hz for 40–60 min.