Energy production from biomass is an alternative and additive way to fossil fuel based energy production to reduce the dependency on limited fossil fuel sources and mitigate the harmful environmental impacts of these systems. One of the major challenges in establishing efficient renewable energy systems is the complex supply chain structure in an uncertain decision environment, various decisions to be made and different conflicting criteria/objectives. This study describes the key issues in decision making for biomass to energy supply chains such as decision levels, uncertainty and sustainability concepts. It also provides a comprehensive review and systematic classification of the current literature on decision making approaches for design, management and operation of biomass to energy supply chains. This study allows readers to identify the decision making methods that satisfy the problem specific requirements and offer a clear vision of the advances in the field.