Forage systems are the major land use and provide essential resources for animal feeding. Assessing the influence of annual forage crop species on net ecosystem CO2 exchange (NEE) is key to develop management strategies that can help to mitigate climate change, while optimizing productivity of these systems. However, little is known about the effect of annual forage crop species on CO2 exchange fluxes, considering separately net CO2 balances during the growth and fallow periods, and species ecophysiological responses. Our study assesses the influence of cereal monocultures vs. cereal-legume mixtures on (1) ecosystem-scale CO2 fluxes, for the whole crop season and separately for the two periods of growth and fallow; and (2) potential sensitivities of CO2 exchange related to short-term variations in light, temperature, and soil water content. This is the first mid-term (seven years) ecosystem-scale CO2 fluxes assessment of an intensively managed forage system in the Pyrenees region. Our results provide strong evidence that cereal-legume mixtures lead to higher net CO2 uptake than cereal monocultures, as a result of higher gross CO2 uptake, while respiratory fluxes did not significantly increase. Also, cereal-legume mixtures favoured a higher voluntary regrowth during the fallow period, which was decisive for the cumulative net CO2 uptake of the entire crop season. Overall, cereal-legume mixtures enhanced net CO2 sink capacity of the forage crop, while ensuring productivity and forage quality.