The end of the Soviet Union and the collapse of its agricultural structures in the early 1990s has induced the abandonment of a large croplands area, which have been recovered by herbaceous plants. This widespread unintended and abrupt land use change took place over 200,000 km2, a large enough scale to impact the continental and global carbon budgets. The goal of this study is to estimate the net biome productivity (NBP) of the abandoned croplands and to assess the soil C storage dynamics due to recent land conversion. The soil C balance and its input (net primary productivity) and output (heterotrophic respiration) fluxes is simulated in a spatially explicit manner with the process-driven natural vegetation/crop model Organizing Carbon and Hydrology in Dynamic Ecosystems-Supra-Thermal Ion Composion Spectrometer prescribed with successive area changes of abandoned croplands during the 1990s. We estimate that regional agricultural abandonment is responsible of a cumulated carbon sink over 1991–2000 of 373 gC m−2, or 64 TgC over the domain considered, which defines a mean annual C sink of 46.7 g C m−2 a−1. Agricultural practices during the former cultivation phase determine a legacy on the C sink following abandonment, which impacts by +37% to −25% according to the practice considered (no tillage, no fertilization, and export of some crop residues). We conclude that futures studies of this regional change in the C cycle should better consider management information in order to refine the NBP estimate.