An analysis of variations in atmospheric CO2 and ecosystem CO2 fluxes in the Northern Hemisphere shows that warmer autumns have been associated with an earlier autumn-to-winter CO2 build-up in the atmosphere. This seems counter-intuitive: warm autumns surely imply long growing seasons and a beneficial effect on terrestrial carbon sinks as trees and plants make more biomass. An explanation is provided by satellite observations and numerical modelling. Enhanced respiration caused by higher temperatures causes carbon losses that offset photosynthetic gains, limiting the potential of these ecosystems to act as carbon sinks. And CO2 loss due to autumn warming may offset most of the increased CO2 uptake during spring. If future warming occurs more rapidly in autumn than in spring, the ability of northern ecosystems to sequester carbon may diminish more rapidly than previously predicted. The carbon balance of terrestrial ecosystems is particularly sensitive to climatic changes in autumn and spring1,2,3,4, with spring and autumn temperatures over northern latitudes having risen by about 1.1 °C and 0.8 °C, respectively, over the past two decades5. A simultaneous greening trend has also been observed, characterized by a longer growing season and greater photosynthetic activity6,7. These observations have led to speculation that spring and autumn warming could enhance carbon sequestration and extend the period of net carbon uptake in the future8. Here we analyse interannual variations in atmospheric carbon dioxide concentration data and ecosystem carbon dioxide fluxes. We find that atmospheric records from the past 20 years show a trend towards an earlier autumn-to-winter carbon dioxide build-up, suggesting a shorter net carbon uptake period. This trend cannot be explained by changes in atmospheric transport alone and, together with the ecosystem flux data, suggest increasing carbon losses in autumn. We use a process-based terrestrial biosphere model and satellite vegetation greenness index observations to investigate further the observed seasonal response of northern ecosystems to autumnal warming. We find that both photosynthesis and respiration increase during autumn warming, but the increase in respiration is greater. In contrast, warming increases photosynthesis more than respiration in spring. Our simulations and observations indicate that northern terrestrial ecosystems may currently lose carbon dioxide in response to autumn warming, with a sensitivity of about 0.2 PgC °C-1, offsetting 90% of the increased carbon dioxide uptake during spring. If future autumn warming occurs at a faster rate than in spring, the ability of northern ecosystems to sequester carbon may be diminished earlier than previously suggested9,10.