Although human papillomavirus (HPV) infection is a major cause leading to the development of cervical intraepithelial neoplasia (CIN), the relationship between genital microbiome and HPV persistence/clearance is not well established. Loop electrosurgical excision procedure (LEEP) is one of standard treatments of CIN 2/3 globally, yet little is known about how the LEEP influence genital microbiota. We conducted a prospective study of 26 patients with CIN2/3 who underwent analysis of cervical microbiome before and after 3 months of LEEP treatment. Cervical swabs were collected, and microbiomes were analyzed by 16S ribosomal RNA gene sequencing. A decrease of cervical microbial diversity was observed after 3 months of LEEP treatment. Notably, a significant shift from community type of a Prevotella-containing and lack of a consistent dominant species to lactobacillus iners dominated microbiome correlated with LEEP. Particularly, Leptotrichia and clostridium were further decreased after LEEP treatment (P = 0.049 and P = 0.002, respectively). Our results suggest that the cervical microbiome is altered after LEEP treatment in patients with CIN2/3. Further studies with larger sample sizes are needed to validate these findings.