Within the framework of the European project EcoBioCap (ECOefficient BIOdegradable Composite Advanced Packaging), aiming at conceiving the next generation of food packagings, we have designed an argumentation-based tool for management of conflicting viewpoints between preferences expressed by the involved parties (food and packaging industries, health authorities, consumers, waste management authority, etc.). The requirements and user preferences are modeled by several rules provided by the stakeholders expressing their viewpoints and expertise. Based on these rules, the argumentation tool computes consensual preferences which are used to parameterize a flexible querying process of a packaging database to retrieve the most relevant solution to pack a given food. In this paper, we recall briefly the principles underlying the reasoning process, and we detail the main functionalities and the architecture of the argumentation tool. We cover the overall reasoning steps starting from formal representation of text arguments and ending by extraction of justified preferences which are sent to the database querying process. Finally, we detail its operational functioning through a real life case study to determine the justifiable choices between recyclable, compostable and biodegradable packaging materials based on stakeholders’ arguments.