Globally, the majority of large-bodied wild mammals are at risk. The modern biodiversity crisis is a major conservation concern because the loss of these animals also means the loss of their ecological roles within communities. Growing evidence suggests mega-mammals have a disproportionate influence on the function of modern ecosystems, although a comprehensive understanding of their role remains elusive. Here, we use the late Pleistocene megafauna extinction as a proxy to examine the changes in the structure and function of a local mammal community after the catastrophic loss of 80% of large-bodied taxa. Hall’s Cave, in the great plains of Texas, has an unparalleled 20 ka geologic record that allows us to characterise the community before and after the extinction event at 13 ka. We employ the null model program PAIRS to evaluate the strength and type of mammal associations over time. The number and strength of interactions yields insights about the cohesion and resilience of ancient and modern ecosystems. We find that ancient ecosystems were more tightly structured than modern ones. Not only did extinct species form significantly more species associations than today, but the average interaction strength was also significantly stronger. Moreover, unlike modern communities, both positive (e.g. predatory-prey) and negative (e.g. competition) interactions were important before the extinction. In particular, extinct carnivores were much more tightly associated with their prey base than modern species. Our results suggest many fundamental aspects of mammalian communities changed with the loss of megafauna at the terminal Pleistocene.