Achillea thracica Velen. Sec. Achillea s.l. [=Sect. Filipendulinae (DC.) Afan.] is a Bulgarian endemic species found in a single population within the country. Endemic species like A. thracica are often under-studied, yet they hold significant potential for the discovery of novel compounds. The goal of this study was to assess the reproductive capacity of A. thracica (pollen and seeds viability) and its reproductive structures, and to characterize the chemical profile and the antimicrobial activity of its essential oil (EO). The male and female generative spheres show that A. thracica reproduces via sexual reproduction. Furthermore, the normal progression of processes leading to pollen and seed formation is essential for fully realizing reproductive capacity. Despite the high fertility observed in the pollen of the target species, seed viability was found to be very low. Further, the female gametophyte of A. thracica is highly influenced by environmental conditions, which directly affect the quality of the seeds produced. Moreover, the lack of alternative reproductive mechanisms, such as apomixis, limits the plasticity of A. thracica populations, reducing their adaptability to environmental changes. Overall, the composition of A. thracica EO was notably different from that of other Achillea species within Sec. Filipendulinae. Santolina and yomogi alcohols and β-eudesmol were the most abundant compounds found in the EO. The strongest antimicrobial activities of A. thracica EO in our study were found against Clostridium perfringens followed by Yersinia enterocolitica and Listeria monocytogenes. With its vigorous growth, unique essential oil (EO) composition, and strong antimicrobial activity, A. thracica demonstrates significant potential for cultivation and development as a high-value crop. Additionally, A. thracica EO can serve as a promising natural source of β-eudesmol, creating opportunities for diverse commercial applications.