Climate change is predicted to lead to more extreme weather events, including changes to storm frequency, intensity and location. Yet the ecological responses to storms are incompletely understood for sandy shorelines, the globe's longest land-ocean interface. Here we document how storms of different magnitude impacted the invertebrate assemblages on a tidal flat in Brazil. We specifically tested the relationships between wave energy and spatial heterogeneity, both for habitat properties (habitat heterogeneity) and fauna (beta-diversity), predicting that larger storms redistribute sediments and hence lead to spatially less variable faunal assemblages. The sediment matrix tended to become less heterogeneous across the flat after high-energy wave events, whereas (beta-diversity) increased after storms. This higher (beta-diversity) was primarily driven by species losses. Significantly fewer species at a significantly lower density occurred within days to weeks after storms. Negative density and biomass responses to storm events were most prominent in crustaceans. Invertebrate assemblages appeared to recover within a short-time (weeks to months) after storms, highlighting that most species typical of sedimentary shorelines are, to some degree, resilient to short-term changes in wave energy. Given that storm frequency and intensity are predicted to change in the coming decades, identifying properties that determine resilience and recovery of ecosystems constitute a research priority for sedimentary shorelines and beyond.