The end-Permian mass extinction (EPME) profoundly shaped shallow marine ecosystems. Although much has been learned about this event based on the body-fossil record, the global infaunal response to the EPME, as represented by ichnofossils, is much less understood. Here we analyze secular changes in ichnodiversity and ichnodisparity from the late Permian to the Middle Triassic based on a global trace-fossil data set. Results show that, in contrast to the body-fossil record, late Permian global ichnodiversity and ichnodisparity maintained their level until the Griesbachian, followed by a sharp loss in the Dienerian. Notably, the Griesbachian shows an unusual dominance of shallower tiers. The discrepancy between the body- and trace-fossil record is interpreted to be the result of the resurgence of widespread microbial matgrounds in the Griesbachian that aided the preservation of surface, semi-infaunal, and shallow-tier ichnofossils. Our study shows that the EPME strongly affected the sediment mixed layer, allowing the preservation of shallower tier trace fossils. The disappearance of the mixed layer in the earliest Triassic may have enhanced pyrite burial in sediments and inhibited its further re-oxidation, therefore impacting sea water sulfate concentrations.