Amphibian populations are experiencing declines globally, many of which are driven by the fungal pathogen Batrachochytrium dendrobatidis (Bd), but different species of amphibians, as well as divergent populations of the same species, can show drastically different responses to Bd invasion. We answer three questions: what are the potential trajectories of amphibian host populations following Bd invasion; how are each of these trajectories influenced by the transmission dynamics and load dynamics governing an amphibian–Bd system; and) how do ecological, evolutionary, and environmental factors affect both Bd transmission and load dynamics, which influence the amphibian hosts’ population levels? We build a general framework that identifies eight population-level trajectories that amphibian populations can take upon Bd invasion that are a result of five different branch points. Each of these branch points is affected by either the transmission dynamics or the load dynamics underlying the system. Integrating relevant disease ecology theory and empirical data, this framework can be used to guide context-dependent management strategies for amphibian populations infected with Bd.