In 2003 the Indonesian Directorate General of Higher Education launched a new strategy with the aim of improving quality, access, and equity in higher education. It was anticipated that providing higher education institutions with an autonomous status would enable them to manage their own organization and sources of income leading to more efficient and effective implementation of academic activities. This article discusses how staff members of eight public universities and polytechnics in Eastern Indonesia make sense of developments towards greater autonomy. The research investigated the perceived rationale for the move towards greater autonomy, and the main challenges and obstacles expected at an institutional and personal level. Positioned within an organizational embeddedness framework, the research identifies three impediments for a readily acceptance of the change: a history of centralized control, a specific institutional “culture”, and questions of local ownership. Consequently the article argues that autonomy in this case is met with ambiguity; it is simultaneously perceived as threatening (job loss, new job requirements, leadership) and as empowering (finally being able to set own institutional objectives).