From ancient times, the essential oils of plants were used for various purposes since their antimicrobial activity was well known. Oils are obtained from different plant parts and are characterized by a specific, intense smell. They consist of numerous secondary metabolites with different properties that are crucial for the survival and adaptation of plants in their environment. In recent years, people's interest in more natural ways of treatment has increased, therefore essential oils alongside their compounds are on the rise. Essential oils of lemon, lavender, and thyme of the chemotype thymol and linalool and the compounds thymol, carvacrol, and thymoquinone have in common their antimicrobial activity against various bacteria that cause serious infections in humans. Since the key components of essential oils are rapidly metabolized in the human microbiome, it is almost impossible to expect their systemic effect. For this reason, this research examined the effect of orally used essential oils of lemon, lavender and thyme of the chemotype thymol and linalool, as well as the compounds found in essential oils: thymol, carvacrol and thymoquinone, which are integral parts of numerous pharmaceutical products. The purpose of this research is to test the antimicrobial activity alongside minimum inhibitory concentration (MIC) of the mentioned essential oils and their compounds on standard strains - bacteria Staphylococcus aureus ATCC 25923, Enterococcus faecalis ATCC 29212 and Pseudomonas aeruginosa ATCC 27853. The results of disk diffusion methods and diffusion methods in wells showed weaker antimicrobial effects of essential oils compared to the tested compounds of essential oils and a surprisingly strong influence of thymoquinone metabolites, which needs to be further investigated.