Introduction: The pandemic has brought about social changes, which may have affected mental health. The purpose of this study was to determine the prevalence of and associations between anxiety, depression, and stress among Peruvian university students during the covid-19 pandemic. Materials and Methods: This was an analytical, multi-centered, cross-sectional study conducted with 2,572 university students from 16 Peruvian cities. Depression, anxiety, and stress diagnoses were obtained with the dass-21 scale (stress alpha: 0.85; anxiety alpha: 0.84; and depression alpha: 0.87). The values were crossed with significant social and educational variables. Results: Anxiety was the most common condition (extremely severe in 4%, severe in 3%, and moderate in 10%). Whereas stress and depression were not associated with the course of studies (p > 0.330 and p > 0.440, respectively), anxiety was lower among students pursuing health-related degrees (p = 0.011). Women showed higher levels of stress (p = 0.040) and anxiety (p = 0.017). Older participants had relatively lower stress (p = 0.002), depression (p = 0.006), and anxiety (p = 0.044) levels. Third-year students had higher depression levels than first-year students (p = 0.011). Conclusions: Significant prevalence levels and associations were identified for the three conditions, which should be monitored to determine their current status, given the possible future occurrence of panic attacks or post-traumatic stress, among other complications.