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<h4>Objective</h4> To identify sociodemographic and educational factors associated with mental health disorders in Peruvian medical students in clinical years. <h4>Methods</h4> Cross-sectional study. We surveyed students from 24 Peruvian medical schools. We defined negative perception of educational environment as having a Dundee Ready Educational Environment Measure score below 100 points; we defined anxiety and depression as having more than 4 points on the Generalized Anxiety Disorder-7 and Patient Health Questionnaire-9 scales, respectively. Poisson regression with robust variance was used to assess the association between negative perception of educational environment and mental health alterations. <h4>Results</h4> Among the 808 participants, the prevalence of anxiety and depression symptoms was 77.6% and 67.3%, respectively. Negative perception of the educational environment was 31.6%. The factors associated with anxiety were being male (PR = 0.95, 95% CI:0.91–0.98), previous medical condition (Prevalence ratios PR = 1.10, 95% CI:1.05–1.16), previous diagnosis of coronavirus disease 2019 (PR = 0.93, 95% CI: 0.93–0.94), being from highlands (PR = 1.11, 95% CI: 1.05–1.16), studying at a national university (PR = 0.90, 95% CI: 0.88–0.92), and negative perception of the educational environment (PR = 1.04, 95% CI: 1.03–1.05), while factors associated with depression were being male (PR = 0.94, 95% CI: 0.93–0.95), previous medical condition (PR = 1.12, 95% CI: 1.08–1.17), type of university (national) (PR = 0.95, 95% CI: 0.95–0.96), and negative perception of the educational environment (PR = 1.11, 95% CI: 1.07–1.16). <h4>Conclusion</h4> We found evidence that during the COVID-19 pandemic anxiety and depression are prevalent among Peruvian medical students. Sociodemographic factors and negative perception of educational environment were associated with the presence of these conditions.