Background: The COVID-19 pandemic impacted global health, particularly the mental health of healthcare workers in low-resource countries like Peru. Aim: To determine the prevalence of depressive, anxiety, and post-traumatic stress symptoms among health workers in Peru throughout the COVID-19 pandemic between December 2021 and August 2022. Methodology: Cross-sectional study on health workers (physicians, nurses, midwives, medical technologists, and healthcare technicians) from Peru selected by non-probabilistic sampling adjusted by post-stratification weights and the Raking method. We evaluate depressive, anxiety, and post-traumatic stress symptoms with Patient Health Questionnaire 9, General Anxiety Disorder 7, and Post-traumatic Stress Disorder Checklist for DSM-5. Results: We evaluated 2,122 participants, of which 72% were women, and the average age was 38 years. The prevalence of depressive symptoms was 18.6% (95%CI 16.6%-20.8%), anxious symptoms were 12.2% (95%CI 10.6%-13.9%), and post-traumatic stress symptoms were 9.3% (95%CI 7.9%-10.9%). Age, sex, and type of health facility were associated with anxiety and depression symptoms, and for post-traumatic stress symptoms, age, and marital status. Conclusion: Our study provides more updated evidence on the mental health situation of healthcare workers. It reveals a significant proportion of workers with evidence of depressive, anxious, or post-traumatic stress problems.