Background: This study aimed to assess the impact of the COVID-19 pandemic in terms of the prevalence of anxiety, depression and stress symptoms in Italian medical students and to identify the associated factors. Design and Methods: A cross-sectional online survey was administered to second-sixth year medical students of the University of Torino, collecting data on the students’ sociodemographics, COVID-19 exposure, anxiety, depression and stress symptoms. Three hierarchical regressions adjusted for age, gender and year of study were executed. Results: The sample size was 1359. The prevalence of anxiety, depression symptoms, moderate perceived stress and severe perceived stress was 47.8%, 52.1%, 56.2% and 28.4%, respectively. The factors associated with mental health symptoms were: being a woman, a family history of psychiatric disorders, living off-site, competitive/hostile climates and unsatisfying friendships among classmates, poor relationships with cohabitants, negative judgment of medical school choice, fear of COVID-19 infection, feelings of loneliness, distressing existential reflections, and a worsening psychological condition related to the pandemic. Being in the fourth or sixth year constituted a protective factor for depression symptoms. Conclusions: Mental health in medical students was associated with both COVID-independent and COVID-related factors. Accessibility to effective interventions must be increased to counteract these changes.