The accomplishment of food/nutrition security for all across sustainable food systems (SFS) is tied to the Sustainable Development Goals (SDGs). SFS is connected to all SDGs via the traditional framework of social inclusion, economic development, environmental safety, inclusivity, and the development of sustainable food systems. We suggest that, for the world to achieve sustainable development, a shift to SFS is necessary to guarantee food/nutrition security for all, while operating within planetary boundaries to protect ecosystems and adapt to and mitigate climate change. Therefore, there is a requirement for original approaches that implement systemic and more participatory methods to engage with a wider range of food system stakeholders. However, the lack of skills and tools regarding novel methodologies for food system transformation is a key obstacle to the deployment of such approaches in practice. In the first part of this review, a summary of some challenges that occur in the governance of food system transformation is given. Through a case study of plant-based proteins and their biological and chemical modification as diets shift towards alternative proteins, we demonstrate that resource-efficient food systems and food waste, through system transformation, are useful in understanding both (i) how food system transformation has ensued and (ii) how the required transformation is prohibited. Finally, we discuss the implications of food system transformation in terms of nutrition and sustainable healthy diets, which are needed to achieve changes in food safety systems in the future. The linkage of food and the environment is evident, focusing on nutrition and sustainable healthy diets. This cannot be accomplished without system change and research towards new foods and, more specifically, new proteins such as plant-based ones and their biological and chemical modification.