BACKGROUND: Few studies have described the clinical characteristics of patients with COVID-19 from ethnic minority groups. Our objective was to evaluate the mortality and incidence rates, clinical characteristics and factors associated with mortality in cases with COVID-19 belonging to the Amazonian indigenous ethnic group in Peru. METHODS: We performed a retrospective cohort study including all cases from COVID-19 among Peruvian people identified as Amazonian indigenous from 07 March to 31 October 2020. We calculated the standardized mortality and incidence ratios using the indirect age-adjusted method to determine the differences between Amazonian Indigenous and the general population. In addition, we used multivariable logistic regression to determine the risk factors for death. RESULTS: A total of 19 018 laboratory confirmed COVID-19 cases were analyzed. Indigenous people had 3.18 (95% CI, 3.13-3.23) times the risk of infection and 0.34 (0.31-0.37) times the mortality risk of the general Peruvian population. Males had 1.29 (1.04-1.61) times the odds of death compared with females and for each year of age, the odds of mortality increased 1.03 (1.03-1.04) times. Cases with respiratory distress had 2.47 (1.96-3.10) times more likely to die. Having an immunodeficiency was 18.7 (6.12-57.00) times more likely to die. DISCUSSION: The Amazonian indigenous population in Peru was strongly affected by COVID-19 compared with the general Peruvian population.