Abstract This paper reports on the temporal variability of carbon dioxide fluxes in the city centre of Arnhem, a middle-sized Dutch city. The fluxes were continuously measured during four years (2012–2016) using the eddy-covariance method. Additionally, continuous meteorological measurements were carried out. We also analysed data from 30-minute traffic counts performed during those years. Results indicate that the city centre of Arnhem is a strong emission source of CO2 compared to many other cities. The measured annual CO2 flux equals about 8.0 kg C m− 2 yr− 1. Heterogeneity within the footprint of the EC tower appeared to have no or only a small influence on the estimated annual and seasonal carbon fluxes. Sector analysis shows that CO2 fluxes are consistently higher in sectors with the highest built-up surface fraction. However, no statistically significant relationship could be determined. Traffic and space-heating related burning of natural gas are the main emission sources. Weekly and diurnal variations in CO2 flux are clearly correlated with traffic intensity, whereas seasonal variation can largely be explained by space heating demand. Partitioning of the total flux into a heating-related and traffic-related flux revealed that space heating accounts for up to 60% to the total flux during winter. Traffic intensity remains more or less constant throughout the year. In summer, when space heating is absent, CO2 emission is almost entirely related to traffic intensity. However, our estimations suggest that human respiration could have a non-negligible share in this. The contribution of the small fraction of urban green in the city centre is probably minimal. The annual emissions for the city centre estimated from our EC measurements are 20–25% lower than those reported for the whole city by the official emission inventory. Climate projections for the Netherlands suggest that in 2050 Heating Degree Days would be reduced by 27% resulting into a 32% reduction of the heating-related emission flux, without a change in fossil fuel use.