This study highlights the role of large-scale physical perturbations in mediating biotic replacements and shows that an environmental disturbance at the Triassic/Jurassic (T/J) boundary correlates with abrupt and substantial changes in the composition of brachiopod communities. Disturbance changed the phylogenetic structure of Early Jurassic brachiopod communities owing to a removal of higher taxa that were abundant in the Late Triassic. A replacement of brachiopod communities through the Rhaetian in the Kössen Basin (Northern Calcareous Alps), related to a combination of habitat tracking and immigration/local extinction events, indicates a high compositional turnover. This turnover is of local nature only because Early Rhaetian communities migrated or tracked their habitats beyond the Kössen Basin and persisted through to the Late Rhaetian in other regions. A siliciclastic interval that is several meters thick with rare brachiopods dated as the earliest Hettangian marks the extinction–survival interval. This interval is coeval with a negative carbon isotope anomaly, implying a correlation with global perturbation of carbon cycle. A rapid brachiopod recovery is indicated by a presence of several distinct communities in late Early and Middle Hettangian that show onshore–offshore differentiation and beta diversity comparable to pre-extinction levels. Analyses of similarities demonstrate that (1) the compositional turnover of brachiopod communities on generic level at the T/J boundary ( R = 0.83) is substantially higher than turnovers between the Rhaetian zones ( R = 0.28–0.57) and between the Hettangian zones ( R = 0.28–0.53), and (2) the turnover at superfamily level at the T/J boundary accounts for differential composition of Rhaetian and Hettangian communities. A global extinction of athyridoid, spondylospiroid and dielasmatoid superfamilies characterized by high-community level abundances during the Late Triassic led to a new assembly of Jurassic brachiopod communities from surviving superfamilies. In addition to persisting rhynchonellids and zeillerioids, Hettangian brachiopod communities were dominated by terebratuloids, spiriferinoids and pennospiriferinoids. These superfamilies were characterized in the Late Triassic by low community-level abundance. We argue for tracking the phylogenetic structure of communities across mass extinction events because a measurement of the turnover in community-level abundance of higher taxa can be highly relevant for estimating the ecologic impact of mass extinctions. Taxonomic extinction rate metrics or diversity measures can be depressed by surviving taxa that do not re-attain their pre-extinction community-level abundance.