In recent years, there has been a growing recognition of the need to ensure sustainability of agri-food systems, covering a variety of stakeholders and activities from production to waste management. Multi-Criteria Decision Assessment (MCDA) have emerged as crucial tools for sustainability assessment, but many do not consider stakeholder perspectives, which prevents their adoption and use. Our projects, NoAW (No Agricultural Waste) and AgriLoop (High-value products from agricultural residues through sustainable chains), address this issue by focusing on innovative valorization routes for agricultural waste by assessing stakeholder impact categories through participatory decision-making. This article proposes a novel methodology integrating computational social choice and argumentation techniques for achieving justified collective decision-making in agri-food systems. This methodology includes a theoretical framework and related tools, which facilitate the identification, analysis, and aggregation of preferences based on justifications.