There has been a growing concern in recent years about the quality of our environment and dependence on fossil fuels to supply the energy needs of the world, which has created an interest in the development of renewable and less polluting energy sources. One of such alternatives is the Biodiesel, which has many advantages relative to the fossil based Diesel, or Petrodiesel, aside from being physically equivalent. We use the real options approach to determine the value of the managerial flexibility that a Biodiesel plant has to switch inputs among different grain commodities. Our results indicate that the option to choose inputs has value if we assume that the future prices follow stochastic processes such as Geometric Brownian Motion and Mean Reversion Models, and can be sufficient to recommend the use of input commodities that would not be recommended the traditional valuation methods. Given that each of these models provides different option values, the choice of model and parameters has a significant impact on the valuation of this class of projects.