ABSTRACT Purpose To evaluate the association between hysteroscopic treatment of cesarean scar disorder (CSDi), clinical improvement, and changes in the endometrial microbiome, as this remains unclear. Methods This prospective observational study included 40 women diagnosed with symptomatic CSDi. Clinical outcomes, including symptom severity and ultrasonographic measurements, were assessed before and after hysteroscopic treatment. Endometrial microbiome analysis using 16S rRNA gene sequencing was performed in a predefined subgroup of 22 patients preoperatively and at 3 months postoperatively. Microbial composition and diversity were analyzed and correlated with clinical findings. Results Hysteroscopic treatment resulted in a significant reduction in isthmocele dimensions and improvement in clinical symptoms across the entire cohort ( p < 0.01). In the subgroup undergoing microbiome analysis, postoperative samples demonstrated a shift from a polymicrobial profile consisting mostly of Clostridia and Bacteroidia to a Lactobacillus ‐dominant microbial profile, accompanied by a decrease in microbial diversity ( p < 0.001). These microbiological changes occurred in parallel with clinical improvement. Conclusions Hysteroscopic treatment of CSDi is associated with favorable clinical outcomes and concurrent alterations in the endometrial microbiome. Although microbiome analyses were performed in a subset of patients, the findings suggest a potential relationship between anatomical correction and microbial environment. Larger, controlled studies are warranted to further elucidate this association.