Carbon emissions in agriculture play a major role in climate change. Modelling studies enable to investigate the impacts of climate change in crops, accounting for soil organic carbon feedbacks and CO2 concentrations. But it is primordial that crop models properly consider the CO2 exchanges at the level of crop rotations beyond the cycle of a single crop. With this goal in mind, we used the outputs of the soil-crop model STICS in its standard pre-parameterized version to model (i) the Gross Primary Productivity (GPP), derived from the autotrophic respiration and the Net Primary Productivity, which is computed through the daily change in plant carbon (C) pools; (ii) the Ecosystem Respiration (RECO), with the autotrophic component being derived from the plant biomass, plant nitrogen concentration and GPP, and the heterotrophic component from the mineralization of residues and organic matter; and (iii) the Net Ecosystem Exchange, equal to the sum of GPP and RECO. The comparison of simulations with field observations indicates that the model is able to simulate accurately daily CO2 fluxes originating from a long-term and diversified crop rotation (efficiency EF equal to 0.79 for GPP, 0.59 for RECO and 0.67 for NEE). Concerning the evaluation of the cumulated fluxes over the 16-year rotation, the model is able to evaluate it accurately for RECO, with a slight underestimation (normalized deviation ND = 15.7%), and very accurately for GPP (ND = 5.12%). But for NEE, the relative overestimation is higher (ND = 62.2%), indicating that a more precise estimation of HR is required to obtain reliable net C budgets. The model also succeeds to capture the trends in the influence of several environmental drivers on CO2 fluxes. It globally proves to be a valuable tool in the investigation of CO2 exchanges of crop rotations in historical and future climatic conditions.