Earth system models (ESMs) simulate a large spread in carbon cycle feedbacks to climate change, particularly in their prediction of cumulative changes in terrestrial carbon storage. Evaluating the performance of ESMs against observations and assessing the likelihood of long-term climate predictions are crucial for model development. Here, we assessed the use of atmospheric CO2 growth rate variations to evaluate the sensitivity of tropical ecosystem carbon fluxes to interannual temperature variations. We found that the temperature sensitivity of the observed CO2 growth rate depended on the timescales over which atmospheric CO2 observations were averaged. The temperature sensitivity of the CO2 growth rate during Northern Hemisphere winter is most directly related to the tropical carbon flux sensitivity since winter variations in Northern Hemisphere carbon fluxes are relatively small. This metric can be used to test the fidelity of interactions between the physical climate system and terrestrial ecosystems within ESMs, which is especially important since the short-term relationship between ecosystem fluxes and temperature stress may be related to the long-term feedbacks between ecosystems and climate. If the interannual temperature sensitivity is used to constrain long-term temperature responses, the inferred sensitivity may be biased by 20% unless the seasonality of the relationship between the observed CO2 growth rate and tropical fluxes are taken into account. These results suggest that atmospheric data can be used directly to evaluate regional land fluxes from ESMs, but underscore that the interaction between the timescales for land surface processes and those of atmospheric processes must be considered.