Objective Analyze clinical factors and non-oncological gynecological diagnoses before and during the initial months of the COVID-19 pandemic. Method Crosssectional study at an Outpatient Gynecology Clinic in Brazil involving medical consultations performed during the pre-pandemic and pandemic periods. The number of visits, prevalence of non-oncological gynecological diagnoses, and clinical-demographic data were analyzed. Parametric continuous variables were evaluated by Student’s t-test and ANOVA tests, non-parametric variables were evaluated by the Mann-Whitney and Wilcoxon tests, and categorical or binary variables were evaluated by chi-square and Fisher’s exact tests. Univariate logistic regression tests were performed, and variables with p ≤ 0.20 were subjected to multivariate logistic regression. Statistical significance was set at p < 0.05. Results There were 1,236 records during the pre-pandemic period and 530 during the pandemic, reflecting a significant reduction (57.88%; p = 0.001) in medical consultations. The outpatient prevalence of women older than 50 y (OR 0.85; 95%CI 0.68–1.05) reduced, and the outpatient prevalence of postmenopausal women with hot flashes (OR 1.34; 95%CI 1.09–1.65; p = 0.005) and alcohol consumption habits (OR 2.76; 95%CI 1.15–6.59; p = 0.023) increased. There was a 6% proportional increase in noninflammatory disorders of the female genital tract (p = 0.030) and a 72.4% decrease in general physical examinations, contraception, and procreation (p = 0.001). Multivariate analysis showed that there was an increased prevalence of abnormal uterine bleeding (OR, 1.7; 95% CI 1.34–2.16; p = 0.001) and endometriosis (OR 1.65; 95% CI 1.13–2.42; p = 0.01). Conclusion Medical consultations for benign gynecological diseases during the pandemic prevented non-inflammatory disorders of the female genital tract, with an emphasis on abnormal uterine bleeding and endometriosis. There was an increased prevalence of women under 50 years of age, women with symptoms of hot flashes, and alcohol consumption habits and a reduction in the prevalence of general physical examinations, contraception, and procreation.