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The deployment of dedicated energy crops and the related land-use change are topical issues, particularly in relation to carbon storage and climate change mitigation effects. In order to maximize their mitigation potential and to fully supply new biorefineries, perennial energy crops may be established, not only on former idle and grazing lands, but also on the least remunerative cropland, as indirect land use change effects are still very uncertain. Possibly becoming a future land-use change option, the carbon flows of the most common crop rotation in Europe (maize-wheat) and the perennial grass switchgrass were measured, and later included in a biogeochemical model to build possible scenarios. Yearly mean soil respiration did not statistically differ between switchgrass and the annual cereals (2.9 and 2.5 Mg CO2 ha(-1) month(-1), respectively), but in switchgrass the peak flux was reached during crop growth (6.1 Mg CO2 ha(-1) month(-1)), while in the cereal system it occurred in bare soil (after harvest and soil tillage) (4.5 Mg CO2 ha(-1) month(-1)). Harvest residues contributing to soil organic matter were highest in maize (12.4 Mg ha(-1) y(-1)) and decreased in switchgrass (-79%) and wheat (-87%). Root biomass was much higher in switchgrass (10.0 Mg ha(-1) y(-1)) than maize (-81%) or wheat (-94%). Model projections showed how continuous switchgrass cycles of 15 years following annual crops cultivation were capable to keep building up SOC inventories (0.24 or 0.32 Mg ha(-1) y(-1)) up to the year 2100. On the opposite, maintaining the land under maize-wheat cultivation, depending on maize stover management, would either produce a SOC loss (-3.6 Mg ha(-1)) or could help the soil increasing SOC (9.4 Mg ha(-1)) towards a new equilibrium after two decades.