Background: We investigated some of the factors associated with depression, perceived stress, and anxiety in clinical and nonclinical healthcare workers of two hospitals. Methods: A mixed-methods approach was used. The sample included clinical (physicians, nurses, and others) and nonclinical (security and cleaning staff) healthcare workers of two tertiary hospitals in Peru. Participants completed an online self-survey. In the qualitative analysis, data were subjected to thematic analysis. Results: We analyzed data from 613 participants, of which 8.6%, 9.0%, and 78.2% had moderate-to-severe anxiety, depression, and perceived stress, respectively. Having a previous mental health problem, being concerned about losing one’s job, having at least two COVID-19 symptoms in the preceding two weeks, and being afraid of infecting family members increased the prevalence of experiencing moderate-to-severe depression and anxiety. The qualitative analysis allowed us to identify five recurring factors that caused a negative impact on workers’ lives during the pandemic: emotional distress linked to hospital experiences of suffering and death, modification of routines, fear of COVID-19, exacerbation of mental disorders, and physical problems associated with emotional distress. Conclusions: Clinical and nonclinical healthcare workers in Peru have experienced depression, anxiety, and stress during the COVID-19 pandemic. Future research and interventions are necessary to improve psychological support for hospital workers.