Biomass supply chains play an important role in providing feedstock for the production of renewable energy and fuels. However, biomass supply chains frequently face a challenge in large-scale uptake due to the lack of cooperation and coordination among supply chain players. This work presents a conflict analysis approach to analyse the effect of relationships among supply chain players within an optimal biomass supply chain. Conflict analysis was previously introduced to analyse the degree of conflict among nations based on several geopolitical issues systematically. In the context of biomass supply chains, conflict analysis can be adapted to model the relationships between supply chain players based on their preferences towards specific issues or policies. A biofuel supply chain case study is solved to demonstrate the applicability of the proposed conflict analysis. In the presented case study, a hypothetical government policy for biofuel supply chains is introduced. Conflict analysis is used to evaluate the preferences of the supply chain players towards the proposed policy and convert these opinions into quantifiable relationships known as the degree of conflict. Results from the conflict analysis are compared with a case where conflict analysis is not considered.