An efficient micropropagation protocol for production of genetically uniform clones of Eryngium campestre L. was developed. To determine the effect of nutritional and hormonal factors on shoot and root development and bioactive compounds production, three variants of media differing in the content of macro- and micronutrients, as well as plant growth regulators of various types and concentrations were tested. The highest regeneration (100%), with over 13 shoots per explant, was induced on Murashige and Skoog (MS) medium with 1.0 mg l−1 benzyladenine (BA) and 0.1 mg l−1 indole-3-acetic acid (IAA). The in vitro derived shoots multiplied through axillary bud formation were rooted and transferred to an experimental plot with 78% frequency of survival. Flow cytometry showed no variation in nuclear DNA between the seedlings and micropropagated plants. Preliminary thin layer chromatography (TLC) analysis indicated that phenolic acids, saponins, flavonoids and acetylenes were present in plant biomass. Ultra high performance liquid chromatography (UHPLC) analysis revealed that shoots and roots from in vitro derived plants and root cultures maintained the ability to produce rosmarinic acid (RA), rosmarinic acid hexoside (RA-HEX) and chlorogenic acid (CGA). The highest phenolic acid content was detected in roots of in vitro regenerated plants. The extract from those roots expressed the highest inhibitory effect against bacteria Staphylococcus aureus, as well as dermatophytes Trichophyton mentagrophytes and T. rubrum.