Retrograde menstruation is a widely recognized etiological factor for endometriosis (EMs); however, it is not the sole cause, as not all affected women develop EMs. Emerging evidence suggests a significant association between the vaginal microbiota and EMs. Nonetheless, the precise mechanisms by which microbial communities influence the pathophysiology and progression of EMs remain unclear. In this study, the cervical mucus from patients with EMs showed significantly greater microbial abundance compared with that of controls, with Streptococcus agalactiae (S. agalactiae) exhibiting the most substantial increase as determined by 16S rRNA gene sequencing. In a murine model, elevated S. agalactiae levels significantly increased the lesion number and colonization, whereas antibiotic treatment reduced lesion formation. Metabolomic analyses showed elevated L-carnitine levels in the cervical secretions and serum of patients with EMs, a finding corroborated in murine tissues. Exogenous L-carnitine administration similarly increased the number and weight of endometriotic lesions. Meanwhile, the inhibition of L-carnitine synthesis suppressed lesion formation induced by S. agalactiae. In vitro, both S. agalactiae and L-carnitine promoted EMs cell proliferation, migration, and invasion. L-carnitine synthesis inhibition attenuated cell motility stimulated by S. agalactiae. Mechanistically, S. agalactiae enhanced angiogenesis through L-carnitine by upregulating vascular endothelial growth factor expression and increasing human umbilical vein endothelial cell motility. These findings identify S. agalactiae as a key cervical microbiome component in EMs development and reveal a microbiota-metabolite-angiogenesis axis that may offer novel therapeutic targets.© 2025. The Author(s).