Microbial communities regulate ecosystem responses to climate change. But predicting these responses is challenging due to complex interactions among processes at multiple ecological scales. Organismal traits that determine individual performance and ecological interactions are essential for scaling up predictions of environmental responses from individuals to ecosystems. We combine experiments and mathematical models to show that key microbial traits—cell size, shape, and cell contents—independently drive shifts in demographic rates across temperatures, having cascading effects on community structure, dynamics, and ecosystem function. Moreover, intra- and interspecific trait variation play distinct, trait-specific roles in temperature responses. These species-level responses scale up to cause predictable, nonlinear shifts in microbial community composition and respiration rates, with direct implications for the effects of warming on the global carbon cycle. Mechanistically linking microbes with climate using traits will help refine predictions about complex ecosystem-climate feedbacks and the pace of climate change.