Warming increases the metabolic demand of consumers1, strengthening their feeding interactions2. This could alter energy fluxes and even amplify extinction rates within the food web. Such effects could simplify the structure and dynamics of ecological networks although an empirical test in natural systems has been lacking. Here, we tested this hypothesis by characterizing around 50,000 directly observed feeding interactions across 14 naturally heated stream ecosystems. We found that higher temperature simplified food-web structure and shortened the pathways of energy flux between consumers and resources. A simple allometric diet breadth model predicted 68–82% of feeding interactions and the effects of warming on key food-web properties. We used model simulations to identify the underlying mechanism as a change in the relative diversity and abundance of consumers and their resources. This model shows how warming can reduce the stability of aquatic ecosystems by eroding the structural integrity of the food web. Given these fundamental drivers, such responses are expected to be manifested more broadly and could be predicted using our modelling framework and knowledge of how warming alters some routinely measured characteristics of organisms.