A common belief is that agricultural fields cannot be net carbon sinks, but perennial tree crops, growing a permanent woody structure with a life cycle of decades could act as carbon sink. Vineyards are good candidates to test this hypothesis, because they are often grown with limited soil cultivation and produce plenty of woody pruning material that can be left on the ground. Three Eddy Covariance sites were established in different vineyards, along a north-south transect, in Italy, to study the role of vine cultivation in the carbon balance of the Italian penisula. The year 2009 was chosen as a reference year for the three sites, in order to compare carbon budget estimates in areas characterized by different meteorological, pedological and geomorphological conditions. In the three sites a carbon sink ranging between 814 (Negrisia site) and 89 (Serdiana site) g C m−2 y−1 was measured. Both climate (water availability and PAR) and management (in particular the presence of permanent grass cover) have a strong impact on the carbon balance of the ecosystems. Even if it can be argued that this sink may be only temporary and the built-up can be substantially disrupted at the end of the vineyard life cycle, these results show that there is a concrete possibility of storing carbon in agricultural soils. Proper practices can be defined to preserve this storage at best, greatly contributing to the global carbon budget.