Since the Sustainable Development Goals (SDGs) came into effect, both UNESCO and other international organisations recommend empowering youth to implement the SDGs in universities. Getting started with the SDGs at university level is of special relevance in pre-service teacher training since future teachers are powerful agents of change in the lives of young people. Future teachers need to acquire competencies in sustainability to be able to promote meaningful changes in sustainable behaviour. To that end, holistic approaches to facilitate their acquirement need to be developed. The aim of this study is to explore which teaching methodologies are suitable for the development of competencies in sustainability in Higher Education (HE) and how to empower students to take a leading role in implementing the SDGs in universities. The participants in the study are a group of 23 students in pre-service teacher training. The experimental educational model used for the development of sustainable competencies consists of a methodological sequence of Project-Oriented Learning (POL) and a Cross-disciplinary Workshop on Sustainable Food. This study provides evidence that a holistic approach is appropriate for developing sustainable competencies and contributes to empowering students to implement SDG 12 at their university.