This study examines the morphological responses of Late Permian brachiopods to environmental changes. Quantitative analysis of body size data from Permian–Triassic brachiopods has demonstrated significant, directional changes in body size before, during and after the Late Permian mass extinction event. Brachiopod size significantly reduced before and during the extinction interval, increased for a short time in more extinction-resistant taxa in the latter stages of extinction and then dramatically reduced again across the Permian/Triassic boundary. Relative abundances of trace elements and acritarchs demonstrate that the body size reductions which happened before, during and after extinction were driven by primary productivity collapse, whereas declining oxygen levels had less effect. An episode of size increase in two of the more extinction-resistant brachiopod species is unrelated to environmental change and possibly was the result of reduced interspecific competition for resources following the extinction of competitors. Based on the results of this study, predictions can be made for the possible responses of modern benthos to present-day environmental changes.