Latin America has emerged as an epicenter of the COVID-19 pandemic. Brazil, Peru, and Ecuador report some of the highest COVID-19 rates. These countries also face dual threats from development challenges and El Niño, which impact local disease ecologies. A country like Peru, e.g., which is highly sensitive to El Niño, already copes with an ecosyndemic burden, i.e., co-occurring multiple infectious diseases, which heighten during climate extreme events. In this commentary, we highlight the importance of El Niño as a major factor that not only may aggravate COVID-19 incidence, but also the broader health problem of ecosyndemics in Latin America.