The possibility of using biomass as a source of energy in reducing green-house gas emissions is a matter of great interest. In particular, biomasse from agriculture represent one of the largest and most diversified sources to be exploited and more specifically, ethanol and diesel deriving from biomass have the potential to be a sustainable means of replacing fossil fuels for transportation. Nevertheless, the cultivation of dedicated energy crops does meet with some criticism (competitiveness with food crop cultivation, water requirements, use of fertilizers, etc.) and the economical and environmental advantages of this activity depend on accurate evaluations of the total efficiency of the production system. This paper illustrates the production potential of two energy crops, sunflower (Helianthus annuus) and maize (Zea mais), cultivated with different water and fertilization supplies in the region of Tuscany, in central Italy. A 50-year climatic series of 19 weather stations scattered around Tuscany was used to run the crop model CropSyst for obtaining crop biomass predictions. The effect of climate change and variability was analyzed and the potential production of bioenergy was investigated in terms of pure vegetable oil (sunflower) and bioethanol (maize). The results demonstrated that despite a reduction in crop yields and an increase of their variability due to climate change, the cultivation of maize in the regional set-aside areas would be capable of supplying approximately 50% of the energy requirements in terms of biofuel for transportation obtained, while the cultivation of a sunflower crops would supply less than 10%.