Although urban areas occupy a relatively small fraction of land, they produce major disturbances of the carbon cycle through land use change, climate modification, and atmospheric pollution. In this study we quantify effects of urban areas on the carbon cycle in Europe. Among urbanization-driven environmental changes, which influence carbon sequestration in the terrestrial biosphere, we account for: (1) proportion of land covered by impervious materials, (2) local urban meteorological conditions, (3) urban high CO2 concentrations, and (4) elevated atmospheric nitrogen deposition. We use the terrestrial ecosystem model BIOME-BGC to estimate fluxes of carbon exchange between the biosphere and the atmosphere in response to these urban factors. We analysed four urbanization-driven changes individually, setting up our model in such a way that only one of the four was active at a time. From these model simulations we found that fertilization effects from the elevated CO2 and the atmospheric nitrogen deposition made the strongest positive contributions to the carbon uptake (0.023 Pg C year−1 and 0.039 Pg C year−1, respectively), whereas, the impervious urban land and local urban meteorological conditions resulted in a reduction of carbon uptake (−0.005 Pg C year−1 and −0.007 Pg C year−1, respectively). The synergetic effect of the four urbanization-induced changes was an increase of the carbon sequestration in Europe of 0.058 Pg C year−1.