Introduction: The prolongation and consequences of the COVID-19 pandemic have led to an uncertain and devastating panorama in many populations, and the evidence shows a high prevalence of mental health problems in medical students. The objective was to evaluate the association between mood disorders and sleep quality (SQ) in Peruvian medical students during the COVID-19 pandemic. Methods: A cross-sectional study was conducted on 310 medical students from a private university in Peru. The SQ was measured using the Pittsburgh Sleep Quality Index (PSQI), while mood disorders were evaluated using the Depression Anxiety and Stress Scale-21 (DASS-21). All information was collected by online surveys and then analysed in the R programming language. Results: The SQ results measured by PSQI were poor in 83.9% of the medical students. In the Poison regression analysis, the results of the bivariate analysis in men show that all mood disorders found the prevalence of poor SQ. However, in the multivariate analysis only stress (PRa = 1.30; 95% CI, 1.08-1.57; P < 0.01) and anxiety (PRa = 1.34; 95% CI, 1.09-1.56; P < 0.01) increased the prevalence of poor SQ. Women had a similar pattern in bivariate analysis, whereas in multivariate analysis, only severe stress (PRa = 1.15; 95% CI, 1.01-1.29; P < 0.05) increased the prevalence of poor SQ. Conclusions: This study allows us to observe the consequences that the COVID-19 pandemic is having on medical students in Peru. It also revealed a population group vulnerable to poor quality of sleep and bad mood, which in the future will impact on health. It is suggested to educate medical students about the importance of proper sleep hygiene and the consequences of poor sleep hygiene practices.