A pilot study investigated cervicovaginal microbial profiles in women with infertility associated with endometriosis prior to frozen embryo transfer (FET). Microbial profiles associated with successful pregnancies had higher relative abundances of Lactobacillus and Bifidobacterium, while Gardnerella, Streptococcus, and Atopobium were more common in failures. Cervical alpha diversity was significantly lower in successful transfers. The LEfSe analysis identified different taxa, such as Peptostreptococcales in successes and Pseudomonadaceae in failures. PICRUST functional analysis showed dysregulated metabolic pathways in failure-associated microbiomes. Cervical microflora showed a higher DMI, indicating greater individual specificity. The findings suggest that cervical microbiota profiling is a promising minimally invasive approach to personalize ART.