Medicinal plants are used in traditional, folk medicine and veterinary practice to treat and prevent exacerbations of chronic diseases, diseases of the cardiovascular and nervous systems, respiratory and digestive organs, liver, bile ducts, kidneys, urinary tract, to regulate metabolism and to boost immunity, etc. The therapeutic effect on the body is exerted by biologically active substances (alkaloids, glycosides, tannins, essential oils, and others) that are present in various parts of plants. Understanding the issue of interaction between the intestinal microbiota and drugs based on medicinal plants will contribute to the development of treatment protocols for various diseases, including chronic ones, by the normalization of impaired functions due to plant origin substances. In this study, we determined the effect of Melissa officinalis, Lavandula angustifolia, Salvia officinalis on the intestinal microbiota of white rats fed a high-fat diet. The addition of 5% crushed young dry shoots of S. officinalis, L. angustifolia, M. officinalis to the high-fat diet of laboratory rats significantly changed the quantitative ratio of Escherichia coli with normal and altered enzymatic properties in the intestinal content. The number of typical E. coli in rats fed with S. officinalis and L. angustifolia decreased by 1.7 and 1.6 times; non-lactose fermenting form of E. coli, on the contrary, increased by 1.8–2.1 times in rats fed with any of the medicinal plants compared to the control. Amid the addition of medicinal plants to the diet, it was not possible to isolate opportunistic enterobacteria of the genus Citrobacter, however, an increase in the number of the genus Candida fungi was observed.