Ecological filters and nutrient heterogeneity are important in the function of ecosystems. Herbaceous layers alter forest ecosystems by filtering tree species during early stages of tree reproduction and influencing nutrient cycling. Important aspects about how tree species successfully establish below and extend above this ecological filter are unanswered in forest ecology. We experimentally tested the effects of large ungulate carcasses on the filtering function of herbaceous layers. Even well-utilized carcasses created unexpected disturbances that reduced herbaceous cover, which effectively perforated the herbaceous layer filter that can differentially influence tree reproduction. Carcasses also created lasting biogeochemical “hotspots” in forest soils that may help maintain plant biodiversity by creating resource heterogeneity and shifting competitive relationships. Because the spatial distribution of carcasses is influenced by predators, these data establish an unrecognized link between large carnivores, prey carcasses, and ecosystem processes. This link supports a novel understanding of disturbance by large herbivores in forest ecosystems by demonstrating an important interaction between predator–prey functional traits and tree seedling dynamics on either side of a major ecological filter.