Understanding the carbon dynamics of the terrestrial biosphere during climate fluctuations is a prerequisite for any reliable modeling of the climate-carbon cycle feedback. We drive a terrestrial vegetation model with observed climate data to show that most of the fluctuations in atmospheric CO₂ are consistent with the modeled shift in the balance between carbon uptake by terrestrial plants and carbon loss through soil and plant respiration. Simulated anomalies of the Fraction of Absorbed Photosynthetically Active Radiation (FAPAR) during the last two El Niño events also agree well with satellite observations. Our model results suggest that changes in net primary productivity (NPP) are mainly responsible for the observed anomalies in the atmospheric CO₂ growth rate. Changes in heterotrophic respiration (R_h) mostly happen in the same direction, but with smaller amplitude. We attribute the unusual acceleration of the atmospheric CO₂ growth rate during 2002–2003 to a coincidence of moderate El Niño conditions in the tropics with a strong NPP decrease at northern mid latitudes, only partially compensated by decreased R_h.