Abstract The COVID-19 pandemic had a delayed onset in South America compared to Asia (outside of China), Europe or North America. In spite of the presumed time advantage for the implementation of preventive measures to help contain its spread, the pandemic in that region followed growth rates that paralleled, and currently exceed, those observed several weeks before in Europe. Indeed, in early August 2020, many countries in South and Central America presented among the highest rates in the world of COVID-19 confirmed cases and deaths per million inhabitants. Here, we have taken an ecological approach to describe the current state of the pandemic in Peru and its dynamics. Our analysis supports a protective effect of altitude from COVID-19 incidence and mortality. Further, we provide circumstantial evidence that internal migration through a specific land route is a significant factor progressively overriding the protection from COVID-19 afforded by high altitude. Finally, we show that protection by altitude is independent of poverty indexes and is inversely correlated with the prevalence in the population of risk factors associated with severe COVID-19, including hypertension and hypercholesterolemia. We discuss long-term multisystemic adaptive traits to hypobaric hypoxia as possible mechanisms that may explain the observed protective effect of high altitude from death due to COVID-19.