Bio-based value chains (BBVCs) have often been criticized for their detrimental social and environmental effects. Existing methods such as social impact assessment do not sufficiently address these negative effects because of their limited focus and lack of attention to social justice. This paper explores the contribution of Capability Sensitive Design (CSD) to designing BBVCs for social justice. CSD is a combination of Value Sensitive Design (VSD), an approach to account for human values in a design process, and the Capability Approach (CA), a normative framework that incorporates multiple dimensions of human well-being. Three case studies demonstrate how CSD can be used to make design choices in the early stages of developing new BBVCs from waste biomass. The cases explore olive oil residues in Spain, coffee and cocoa residues in Colombia, and encroacher bush in Namibia. CSD is a relatively new approach and its contribution to social justice in BBVCs remained unexplored. We show that CSD can contribute to distributive, recognition, and procedural justice by allowing the identification of local vulnerable stakeholders and providing tools to connect their needs, knowledge, and capabilities to concrete design choices.