Respiratory release of CO2 by microorganisms is one of the main components of the global carbon cycle. However, there are large uncertainties regarding the effects of climate warming on the respiration of microbial communities, owing to a lack of mechanistic, empirically tested theory that incorporates dynamic species interactions. We present a general mathematical model which predicts that thermal sensitivity of microbial community respiration increases as species interactions change from competition to facilitation (for example, commensalism, cooperation and mutualism). This is because facilitation disproportionately increases positive feedback between the thermal sensitivities of species-level metabolic and biomass accumulation rates at warmer temperatures. We experimentally validate our theoretical predictions in a community of eight bacterial taxa and show that a shift from competition to facilitation, after a month of co-adaptation, caused a 60% increase in the thermal sensitivity of respiration relative to de novo assembled communities that had not co-adapted. We propose that rapid changes in species interactions can substantially change the temperature dependence of microbial community respiration, which should be accounted for in future climate–carbon cycle models.