High-throughput sequencing reveals that organs once considered sterile, such as the endometrium, actually harbor distinct microbial communities. These organ-specific microbiota play critical roles in disease pathogenesis, including cancer. Nevertheless, defining a healthy endometrial microbiota remains challenging due to inconsistent compositional profiles reported across studies. Furthermore, although endometrial dysbiosis has been linked to endometrial cancer (EC), multiple confounding factors influence specific microbial signatures, and the causal relationship between these microbes and EC pathogenesis remains a topic of debate. This review aims to systematically examine current research on the endometrial microbiota, analyze the factors contributing to discrepancies in study findings, and elucidate the potential interaction mechanisms between the endometrial microbiota and EC.