Abstract Stem respiration is a key driver of carbon flux from ecosystems to the atmosphere, yet its response to global warming remains poorly constrained. In particular it has been proposed that stem respiration acclimates to changing temperatures, which could have large implications for carbon cycling under climate change, but no theory exists to predict acclimated respiration rates. Here, we hypothesized that stem respiration is physiologically linked to transpiration in order to maintain hydraulic continuity. We then use that linkage, combined with Eco-evolutionary optimality theory, to develop a theoretical prediction of the temperature sensitivity of both acclimated and instantaneous stem respiration. Leveraging an extensive global dataset, we observe temperature sensitivities of stem respiration across geographical and seasonal variations that are consistent with this prediction. Our findings reveal that stem respiration contributes approximately a quarter of the global above-ground auto-trophic respiration, with an estimated annual emission of around 11.20 ± 5.88 Pg C—comparable to total anthropogenic emissions. Importantly, incorporating thermal acclimation of stem respiration into projections significantly reduces predicted land ecosystem carbon emissions by 4.41 and 9.56 Pg C under the SSP126 and SSP585 scenarios, respectively, for the 21st century.