The growing interest surrounding bioenergy programs calls for researchers to move from the rhetoric to advance research for specific sustainability issues confronting bioenergy as a viable renewable energy option. This research focuses on the development of a methodology for the sustainability assessment of biomass to energy supply chain. It presents the development of a theoretical framework used to identify stages where sustainability is expressed in relation to a number of measurable indicators representing environmental and socio-economic impact on the biomass to energy supply chain. Additionally, the developed methodology employs Analytic Hierarchy Process (AHP) as a method to capture and present expert’s opinion in the weighting of the sustainability indicators. The assessment of sustainability is based on an aggregate index that considers the individual stages of the bioenergy supply chain. A fictitious case study is presented to demonstrate the utility of this methodology. The research proposes an extended view of biomass to energy supply chain focusing on life cycle assessment and systems theory approaches with due consideration for the sustainability pillars. The proposed method is suitable for wood pellet supply chain and can also be employed in the sustainability assessment of other feedstocks.