Summary: The paradigm of sterility in the upper female reproductive tract has been revised in recent years thanks to advanced next-generation sequencing (NGS) techniques. It is now understood that the microbiota of the female reproductive tract represents a continuum, playing a critical role in maintaining homeostasis, regulating the immune response, and protecting against pathogens. A healthy vaginal ecosystem is dominated by Lactobacillus spp., whereas dysbiosis—characterized by a decrease in lactobacilli in favor of anaerobic flora (bacterial vaginosis) or aerobic flora (aerobic vaginitis) – predisposes to a range of complications. Current state-of-the-art analysis indicates a significant impact of the vaginal microbiota on the risk of preterm birth, as well as the association of specific taxa (e.g., Sneathia, Prevotella) with human papillomavirus (HPV) infection complications and the progression of cervical intraepithelial neoplasia (CIN). Furthermore, recent evidence confirms that the uterine cavity harbors its own unique microbiota. A Lactobacillus-dominated profile in the endometrium strongly correlates with higher rates of embryo implantation and live births in in vitro fertilization (IVF) procedures, whereas the presence of pathogens and chronic endometritis (CE) are linked to reproductive failures. Additionally, female reproductive health is influenced by the gut microbiota through the gut-reproductive axis. Disruptions of the estrobolome, along with the endotoxemia and leaky gut hypotheses, underlie novel pathomechanisms in conditions such as endometriosis and polycystic ovary syndrome (PCOS). This paper provides an exhaustive summary of contemporary knowledge regarding the relationship between the microbiome and female reproductive health, encompassing innovative therapeutic approaches, including probiotic therapy, targeted biotherapeutics, and vaginal and fecal microbiota transplantation (VMT, FMT).