The application of continuous improvement initiatives such as Lean in Higher Education Institutes is an emerging topic for research, as these organizations are increasingly adopting the tools and methods to improve their quality practices. Nevertheless, Institutes of Higher Education differ significantly from business organizations, which limits the applicability of previous research findings. Using Q-methodology, the present study examines the prevailing perspectives on critical success factors of Lean at Dutch and Belgian Institutes of Higher Education. Findings show that Lean implementation at Institutes of Higher Education takes place bottom-up, with relatively little management involvement and commitment, and mostly involves supporting processes. This impedes the organizational culture change that needs to take place for Lean implementation to be sustainable in the long term, as successes are less visible to management, leading to less management involvement. However, as this is due to structural difference of Higher Education from other industries, it requires a different approach than the conventional, top-down approach prescribed in the literature. A bottom-up implementation of Lean is recommended, centered on improving university-wide supporting processes, promoting cross-departmental cooperation, and overcoming the silo mentality.