Until recently, it was assumed that the pathogenic fungus Batrachochytrium dendrobatidis (Bd) was not widely distributed in warm ecosystems such as lowland tropical rainforests because high environmental temperatures limit its growth. However, several studies have documented Bd infection in lowland rainforest amphibians over the past decade. In addition, a recent study focusing on museum-stored specimens showed that Bd has been present in the lowland Amazon for more than 80 years. These findings lent support to the idea that some lowland rainforest habitats offer suitable environmental conditions for Bd growth, even though most lowland areas may contain suboptimal conditions limiting the pathogen spread and growth. Here, we surveyed four sites in southeast Peru to examine the prevalence and the intensity of infection of Bd in lowland Amazonian amphibians and to fill a gap between two areas where Bd has been present for more than a decade. In one of these “hotspots” of Bd infection, the upper slopes of Manu National Park, several species experienced population declines attributed to Bd epizootics over the past 15 years. We also examined the thermal profile of the main microhabitats used by lowland Amazonian frogs to infer whether these microhabitats offer suitable thermal conditions for Bd growth. We detected Bd in nine lowland frog species and variation in prevalence of infection across years. Our findings suggest that the temperatures in the leaf litter and understory vegetation of some habitats offer suitable conditions for Bd growth.