AIMS: Endometriosis (EM) is a chronic inflammatory disorder with multifactorial etiologies (i.e., genetics and environmental factors, hormonal and immunological changes, and microbiome alterations). The complement system is one of the most frequently dysregulated pathways in EM. Mannose-binding lectin (MBL), a carbohydrate pattern recognition molecule, is the first described recognition subcomponent of the complement lectin pathway (LP). Here, we unveiled the interplay among MBL polymorphisms, plasma levels, LP functionality, and microbiota as potential contributors to EM pathogenesis. MATERIALS AND METHODS: A cohort of 38 EM patients and 20 healthy controls was enrolled, and the levels and functionality of the LP were assessed via ELISA. MBL genetic variants and the endometrial and vaginal microbiome were investigated and correlated. KEY FINDINGS: High MBL levels were related to the disease severity, although not accountable for the MBL2 genotype. MBL and MASP-2 were present in the uterine mucosa but appeared to have no activity at the endometriotic lesion. EM patients with LP functional deficit displayed pathogenic bacterial species more frequently in the endometrial microbiome. Moreover, women affected by EM showed a higher frequency of rare gene variants in the estrogen pathway genes, potentially affecting MBL plasma levels. SIGNIFICANCE: A lower functionality of LP in the uterine mucosa may contribute to an unbalanced bacterial environment that could activate endometrial cells. Not only the genotype and the inflammatory condition, but also the estrogen pathway can cause altered MBL levels, thus contributing to changes in the LP functionality.