Since the last Ice Age (ca 115 000–11 700 years ago), the geographical ranges of most plants and animals have shifted, expanded or contracted. Understanding the timing, geographical patterns and drivers of past changes in insect communities is essential for evaluating the biodiversity implications of future climate changes, yet our knowledge of long-term patterns is limited. We applied a network modelling approach to the recent fossil record of northwestern European beetles to investigate how their taxonomic and trait composition changed during the past 16 000 years. We found two major changes in beetle faunas 4000–3500 and 10 000–9500 years ago, coinciding with periods of human population growth in the Late Holocene and climate warming in the Early Holocene. Our results demonstrate that humans have affected insect biodiversity since at least the introduction of agropastoralism, with landscape-scale effects that can be observed at sites away from areas of direct human impact.