The use of imported fossil fuels for energy purposes across Europe has lead to high dependency and environmental degradation, calling the attention for the need of more sustainable and renewable forms of energy sources. The highest potential of Hungary lies on biomass; however, its use implies not only prosperous but also negative effects. This work introduces a flexible tool-set with dynamic and feedback regional features to quantify such effects and therefore supporting decision making. Through a structured problem and SWOT analyses, the objectives could be structured and their relative importance could be established. Specific indicators were derived and calibrated to measure future regional conditions. A system dynamics model was then built and calibrated using the Vensim software, representing relevant regional processes governing energy fluxes and its related effects. The indicators resulting from simulating empirical scenarios of future sustainable biomass-to-energy processes were implemented into the objective system at selected points in time and in this way the level of sustainability achievement could be assessed. Analyzing the results, it is observed that all case scenarios stress quantitatively the advantages of regional use of biomass by emphasizing sustainability and value added. These results indicate that the developed model is an attractive and flexible toolset for authorities and stakeholders dealing with regional or national energy strategy decisions.