Using biowaste as a resource is required in order to meet the EU common objectives for waste management. Biowaste management should be considered from the economic, environmental, and social perspectives. The resulting complexity constitutes an important barrier to the implementation of biowaste planning projects. The goal of this study is to propose an effective tool to assess, compare, and select the best biowaste management alternatives for stakeholders. In order to reach research goal a methodological approach based on the combination of Multi-Criteria Analysis and System Dynamics method is proposed. The aim of the proposed method implemented in a modelling tool is mainly addressed to policy and decision makers specifically (1) to evaluate biowaste management options, (2) to assess the sustainability of bioenergy projects, and (3) to find an optimal solution for biowaste treatment given the conditions in a particular region. The proposed method can help to structure and assess complex problems while both responding to the interests of multiple stakeholders and avoiding the weaknesses of other evaluation techniques. The method has been applied to a case study involving the three Baltic States – Latvia, Lithuania and Estonia. The results obtained showed that separate collection and Anaerobic Digestion of biowaste is the best solution in all three Baltic States. Other acceptable options include incineration with energy recovery and Mechanical Biological Treatment with Anaerobic Digestion.