Effects of climate change on natural ecosystems can be mediated by ecological processes, but also by rapid evolutionary adaptations and/or non-heritable trait changes in organisms. So far, most studies testing the importance of inter- versus intraspecific changes for how communities and their functioning responds to climate change are either short-term laboratory experiments in highly controlled (artificial) environments, or long-term field surveys suffering from lack of experimental manipulation. Here, we quantified how community composition and functioning has changed in response to long-term warming, including the potential direct and indirect effects via immediate and delayed physiological, non-heritable plastic, ecological, evolutionary and eco-evolutionary responses. We used a site-for-time approach, sampling sites in an artificially heated basin and a nearby area to quantify how >30 years of experimental warming in situ affects benthic grazer communities and traits of grazer taxa, as well as their contribution to a key ecosystem function: grazing on filamentous algae. The community composition shifted with warming, because a non-native species was highly common, and taxa with higher mobility, became more common in the heated areas compared to the control sites. Warming altered community functioning but the underlying mechanisms varied between traits: increased metabolism was caused by intraspecific trait change, while increased grazing rate was mainly driven by species turnover. Our results suggest that both population- and community-level processes mediate the responses of natural communities to long-term environmental change, and that the ongoing warming of coastal waters is likely to alter the functioning of key marine ecosystems.