Lemon beebalm (Monarda citriodora Cerv. ex Lag.) is a well-known source of thymol and other active ingredients with recognised antimicrobial properties. However, no previous research investigated the chemical variability of M. citriodora organs during plant phenology. In this paper, above-ground organs of lemon beebalm harvested during three phenological stages were studied for the content and composition of essential oil (EO) and phenolic compounds as well as antimicrobial and antioxidant activity. The EO content in leaves and inflorescences during the full flowering stage was 3.34% and 3.83%, respectively. The phenological stage of plants mainly influenced the content and chemical composition of EO in leaves. The main component of the EOs both from leaves and inflorescences was thymol (52.63–61.83%). The EOs from these organs collected at the full flowering stage inhibited the growth of all the tested microbial strains at the concentration range 0.156–0.625 µL × mL-1. Plant organs differed in the content of total phenolics, flavonoids, and individual phenolic compounds. The effect of phenological stage on these contents was more pronounced in leaves and stems than in inflorescences. Total flavonoid content in stems and inflorescences was higher than in leaves. Leaves harvested during vegetative stage were characterised by the highest level of linarin, a flavone glycoside (80.66 mg × 100 g-1 of dry raw material). All the tested parts of plants were found to be rich in rosmarinic acid, in particular inflorescences (507.41 mg × 100 g-1). The identified high antimicrobial and antioxidant activity of the studied EOs and extracts can be explained by the high content of thymol in EO and rosmarinic acid in the aerial parts of plants.