Afforestations can be considerable carbon (C) sources due to C losses from the soil after site preparation for tree planting and decreased primary production. In this study, the transition from grassland to afforestation was investigated using two eddy flux towers, which were operated in parallel for 3 years, one on a young afforestation and one on an adjacent grassland. Differences between the fluxes at the two sites were attributable to the management of the sites, without confounding influences of meteorological variability. Site preparation with deep ploughing of the planting rows destroyed 30% of the grassland vegetation at the afforestation site and reduced gross primary productivity by 41% in the first year. At the afforestation site 38 g m−2 less C was sequestered compared with the nonafforested grassland during the first year. In the following years, the C sink at the afforestation site was higher than at the grassland indicating that soil C loss due to site preparation and land use change on the afforestation occurred only during the first year. Metrological conditions, especially summer drought, caused a high interannual variability of the C balance: both sites were small C sources in 2005 (67 g C m−2 a−1 at the grassland and 19 g C g−1 a−1 at the afforestation site) and small C sinks in 2004 and 2006 (−72.5 and −16 g C m−2 a−1 at the grassland and −34 and −61 g C g−1 a−1 at the afforestation). Sheep grazing and mowing affected the short-term dynamics of the C balance and sheep grazing accelerated the C turnover on the grassland site. The investigated afforestation site did not provide any short-term way of sequestering additional C even though soil C losses during the first 3 years were relatively small.