The use of renewable energy in Europe offers the possibility of reducing greenhouse gas emissions, and contributes to energy security and independence. With the reform of the Common Agricultural Policy (CAP) and a variety of recently introduced national directives supporting renewable energy sources in the European Union, the economic attractiveness of bioenergy production has distinctly increased. This article combines an economic evaluation of biomass production with site-related natural conditions of the Havelland region, situated in the north-east area of Germany. Two methods for evaluating site-specific potential biomass yields were compared. For three example biomass crops, evaluations of yield estimations at agricultural lots for site-optimized suitability (SOS) and conventional suitability (CS) were carried out. Both modelling approaches were compared. The results of the GIS modelling indicate that the financial support for increasing the use of renewable energy with the German feed-in system, called Erneuerbare-Energien-Gesetz (EEG), will possibly lead to an increased cultivation of crops with high biomass output. This monocultural orientation of farming practices and the negative effects on the ecosystem could act in opposition to other environmental initiatives of the EU. The outputs of the SOS analysis show that high biomass production could be integrated into environmental policy proposals. Therefore, new EU policy should take modified subsidies into consideration in order to avoid developing conflicts between small-scale changes in landscape ecosystems caused by large-scale transformations in energy policy.