Objective: Endometriosis may negatively affect the ovarian reserve, and also endometriosis surgery may cause further damage to the ovarian reserve. There is lack of definite data for the effect of endometriomas and treatments on the ovarian reserve over time. This study aims to determine the effects of endometrioma and its treatment modalities on ovarian reserve. Design: Prospective cohort study Setting: Turkey tertiary hospital Population: Eighty women with endometrioma diagnosed by ultrasonography and 20 healthy age-matched women as the control group were enrolled in this prospective study. Patients in the study group were divided into four subgroups (20 patients for each group). Methods: Treatment modalities for each study group were expectant management, oral contraceptive (OCP), dienogest, and surgery. All patients were evaluated with ultrasonography, and blood samples were taken during recruitment for anti-mullerian hormone (AMH) values. Additional assessments were done six months after the first assessment. Main Outcome Measures: Prospectively compare the rates of change over time in AMH levels, a reliable ovarian reserve marker, between patients with endometriomas left intact and healthy controls, as well as between patients treated with OCP or dienogest and those who underwent surgical excision due to pain symptoms Results: The median rate of decline in serum AMH levels were 19% in the expectant management group, 26% in the OCP, 21% in the dienogest, 38% in the surgery, and 8% in the healthies. Thus, the rate showed a significant difference between the OCP therapy and healthy control groups (p=0.034) and the surgery and healthy control groups (p=0.001). Multivariate logistic regression analysis suggested that only age was correlated with the rate of decline. Conclusion: Our study is the first in the literature to report on the impact of different endometrioma treatment modalities on ovarian reserve. Our results indicate that surgical intervention is the most harmful treatment while others result in a slight decrease in ovarian reserve. Trial Registration Number: Clinical Trials, NCT03620838