Studies of the end-Permian mass extinction have emphasized potential abiotic causes and their direct biotic effects. Less attention has been devoted to secondary extinctions resulting from ecological crises and the effect of community structure on such extinctions. Here we use a trophic network model that combines topological and dynamic approaches to simulate disruptions of primary productivity in palaeocommunities. We apply the model to Permian and Triassic communities of the Karoo Basin, South Africa, and show that while Permian communities bear no evidence of being especially susceptible to extinction, Early Triassic communities appear to have been inherently less stable. Much of the instability results from the faster post-extinction diversification of amphibian guilds relative to amniotes. The resulting communities differed fundamentally in structure from their Permian predecessors. Additionally, our results imply that changing community structures over time may explain long-term trends like declining rates of Phanerozoic background extinction.