Background/Objectives: Emerging evidence links vaginal microbiome dysbiosis with HPV persistence and CIN progression, but whether microbiome markers provide incremental prognostic value beyond molecular triage assays remains unclear. This study aimed to evaluate whether Lactobacillus depletion and Shannon diversity improve prediction of biopsy-confirmed CIN2+ and CIN3+ outcomes beyond CINtec and HPV-16 genotyping. Methods: This was a secondary analysis of a cross-sectional study including 82 women undergoing cervical screening or follow-up for abnormal cytology. Associations with CIN2+, CIN3+, and CINtec positivity were estimated using modified Poisson regression. Multiplicative interaction between HPV-16 and Lactobacillus depletion was formally tested. Incremental discriminative performance was assessed using area under the receiver operating characteristic curve (AUC), DeLong’s test, net reclassification improvement (NRI), and integrated discrimination improvement (IDI). Results: HPV-16 was the strongest predictor of CIN2+ (PR = 6.08, p < 0.001) and CIN3+ (PR = 5.53, p = 0.001). A significant sub-multiplicative interaction indicated that Lactobacillus depletion carried its strongest prognostic signal in HPV-16-negative women (CIN3+: PR_interaction = 0.04, p = 0.003). Adding microbiome markers to CINtec + HPV-16 significantly improved CIN2+ discrimination (ΔAUC = 0.034, p = 0.031), driven by correct downward reclassification of non-events (NRI_non-events = 0.833). When added to HPV-16 + age, IDI for CIN2+ reached 0.092 (p = 0.004). Conclusions: Vaginal microbiome markers, particularly Lactobacillus depletion, provide statistically significant incremental discriminative value for CIN2+ beyond CINtec p16/Ki-67 dual staining and HPV-16 genotyping. Microbiome-based triage may be most impactful in HPV-16-negative women.