Methane (CH4) and carbon dioxide (CO2) are the dominant gaseous end products of the remineralization of organic carbon and also the two largest contributors to the anthropogenic greenhouse effect. We investigated whether warming altered the balance of CH4 efflux relative to gross primary production (GPP) and ecosystem respiration (ER) in a freshwater mesocosm experiment. Whole ecosystem CH4 efflux was strongly related to temperature with an apparent activation energy of 0.85 eV. Furthermore, CH4 efflux increased faster than ER or GPP with temperature, with all three processes having sequentially lower activation energies. Warming of 4 °C increased the fraction of GPP effluxing as CH4 by 20% and the fraction of ER as CH4 by 9%, in line with the offset in their respective activation energies. Because CH4 is 21 times more potent as a greenhouse gas, relative to CO2, these results suggest freshwater ecosystems could drive a previously unknown positive feedback between warming and the carbon cycle.