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 the assimilation of more than 1 year of atmospheric in situ concentration measurements, we compare the performance of two established data assimilation models, CarbonTracker and TM5-4DVar (Transport Model 5 - Four-Dimensional Variational model), 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° x 4° longitude-latitude grid. Harmonizing the input data allows for analyzing the strengths and weaknesses of the two approaches by direct comparison of the modeled concentrations and the estimated fluxes. We further assess the sensitivity of the two approaches to the density of observations and operational parameters such as the length of the assimilation time window. Our results show that both models provide optimized CO2 concentration fields of similar quality. In Antarctica CarbonTracker underestimates the wintertime CO2 concentrations, since its 5-week assimilation window does not allow for adjusting the distant surface fluxes in response to the detected concentration mismatch. Flux estimates by CarbonTracker and TM5-4DVar are consistent and robust for regions with good observation coverage, regions with low observation coverage reveal significant differences. In South America, the fluxes estimated by TM5-4DVar suffer from limited representativeness of the few observations. For the North American continent, mimicking the historical increase of the measurement network density shows improving agreement between CarbonTracker and TM5-4DVar flux estimates for increasing observation density.