Globalisation and transition from a production-based to a knowledge-based economy have a profound impact on the role and value of higher education in Malaysia. The restructuring and transformation of higher education in Malaysia, particularly in the research universities, focus on critical areas such as research and innovation, teaching and learning, and industry and community engagement, are likely to affect these institutions as a whole and in particular both staff and students. The purpose of this study is to profile the mental health and wellbeing of undergraduate students of the designated research university as the university underwent institutional transformation. The findings from Phase I and Phase II of the study over the course of 2 years and using the New Mind Maps instrument suggest that undergraduate students who were exposed to the changing environment resulting from the university's transformation were experiencing a psychologically stressful and anxiety-provoking time. Implications from the findings are discussed.