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Multinational enterprises (MNEs) in the agri-food sector are continuously transforming their global value chains (GVCs) to address sustainable development challenges of food security (SDG2) and climate change (SDG13). However, the central role of non-governmental organisations (NGOs) in (re)creating GVCs across multilevel stakeholders through innovative approaches to solve sustainability challenges remains under investigated. This explorative study investigates how international NGOs influence the transformation of large-scale industrial animal agriculture to a more sustainable (cell-based) agri-food GVC. The authors conducted a case study on the Good Food Institute (GFI), an international NGO, that has been an active player in the transition to alternative sources of protein to solve animal-based agriculture sustainability issues. The results show that an international NGO can contribute to the transition to a more sustainable GVC and can enhance the GVC’s innovation capabilities.