Endometriosis is a persistent gynaecological disease state marked by development of endometrial-like tissue exterior to the uterus, which triggers pelvic discomfort, chronic inflammation, and fertility issues. Although it has been associated with hormonal imbalances and immune dysfunction, emerging research describes a major role for the microbiota in initiating and accelerating the disease. Disruptions in the gut microbiota have been associated with immune system activation and inflammatory signaling, which may intensify development of endometrial lesions. This review delves into recent findings on how microbial imbalances contribute to the inflammatory landscape of endometriosis, emphasizing the involvement of specific microbial species in influencing estrogen pathways and immune regulation. Therapies centred on probiotics especially strains like Lactobacillus and Bifidobacterium are gaining attention for their potential to rebalance the microbiota, strengthen epithelial barriers and mitigate inflammation. Also, the gene expression studies have shed light on molecular mechanisms affected by microbial alterations, revealing new biomarkers and therapeutic targets. These insights highlight the growing relevance of microbiome research in deepening our understanding of endometriosis and refining its treatment. This review is novel in its comprehensive integration of microbiome, immunological, and molecular insights into endometriosis, and it highlights the potential of microbiota-based diagnostics and individualized probiotic strategies as innovative clinical interventions beyond conventional hormone-centred approaches.