The amphibian fungal disease chytridiomycosis, caused by Batrachochytrium dendrobatidis (Bd), poses a great threat to global amphibian biodiversity. In Peruvian cloud forests of the Kosñipata Valley of Manu National Park where chytrid infection is highly prevalent, we have monitored species-rich amphibian communities since 1996. An epizootic of chytridiomycosis is thought to have caused the disappearance of 35% of species richness in the early 2000s. We investigated the post-epizootic Bd prevalence and infection intensity within the remnant amphibian community from 2008 to 2015, and modeled Bd dynamics as a function of species, season, reproductive mode, life stage, and elevation. Prevalence was higher in 2012–2015 than in 2008–2009, but overall prevalence has remained fairly constant (~50%) post-epizootic. We also found that while prevalence decreased with elevation during the wet season, it generally increased with elevation during the dry season, potentially due to seasonal changes in temperature and precipitation. In aquatic habitats, Bd is likely maintained through a single, stream-breeding, putative reservoir species (which survived epizootics, in contrast to other aquatic-breeding species). The now-dominant terrestrial-breeding species allow Bd to persist and spread in terrestrial habitats, possibly through individual dispersal into naïve areas. We conclude that Bd prevalence in the Kosñipata Valley has stabilized over time, suggesting that Bd is now enzootic. Long-term monitoring of host infection is important because temporal changes in prevalence and infection intensity can cause changes in host species richness and abundance, which in turn may alter the trajectory of host–pathogen dynamics. Abstract in Spanish is available with online material.