Motivation for the study. To document the evolution of COVID-19 in rural Amazonian populations, which are still little known. Main findings. COVID-19 spread rapidly through rural communities, initially spreading to mestizo hamlets and later affecting indigenous communities. Rural mortality varied by region and ethnicity. Social distancing was difficult, and travel to receive government vouchers contributed to contagion. Implications. Identifying the factors that contributed to contagion and the barriers to the adoption of protective measures in rural Amazonian populations will help to face future pandemics. To analyze the evolution of COVID-19 in rural populations of Loreto and Ucayali in the early stage of the pandemic. A community-level longitudinal observational study was conducted and based on two rounds of telephone surveys with local authorities of more than 400 indigenous and non-indigenous rural communities in Loreto and Ucayali, in July and August 2020. We collected information on cases and deaths by COVID-19 in their communities, protective measures adopted and if state assistance was received in the early stage of the pandemic. Descriptive statistics allowed us to evaluate the evolution of the pandemic after the initial outbreak and compare the trends of the two regions, as well as between indigenous and non-indigenous populations. In July 2020, COVID-19 had reached 91.5% of the communities, although deaths from COVID-19 were reported in 13.0% of the communities, with rural mortality being higher in Ucayali (0.111%) than in Loreto (0.047%) and in non-indigenous communities. By August, prevalence decreased from 44.0% to 32.0% of communities, but became more frequent in indigenous communities, and those in Ucayali. Traveling to the city to receive state bonuses and difficulties maintaining social distancing contributed to the spread. Our findings show the evolution of COVID-19 in rural communities and point to important areas of attention in future public policies, for the adoption of protective measures and reconsidering strategies for the distribution of assistance in the face of future pandemics. Motivation for the study. To document the evolution of COVID-19 in rural Amazonian populations, which are still little known. Main findings. COVID-19 spread rapidly through rural communities, initially spreading to mestizo hamlets and later affecting indigenous communities. Rural mortality varied by region and ethnicity. Social distancing was difficult, and travel to receive government vouchers contributed to contagion. Implications. Identifying the factors that contributed to contagion and the barriers to the adoption of protective measures in rural Amazonian populations will help to face future pandemics.