Data assimilation systems allow for estimating surface fluxes of greenhouse gases from atmospheric concentration measurements. Good knowledge about fluxes is essential to understand how climate change affects ecosystems and to characterize feedback mechanisms. Based on assimilation of more than one year of atmospheric in-situ concentration measurements, we compare the performance of two established data assimilation models, CarbonTracker and TM5-4DVar, for CO2 flux estimation. CarbonTracker uses an Ensemble Kalman Filter method to optimize fluxes on ecoregions. TM5-4DVar employs a 4-D variational method and optimizes fluxes on a 6° × 4° longitude/latitude grid. Harmonizing the input data allows analyzing the strengths and weaknesses of the two approaches by direct comparison of the modelled concentrations and the estimated fluxes. We further assess the sensitivity of the two approaches to the density of observations and operational parameters such as temporal and spatial correlation lengths.