This study aims to analyze, investigate the implications, and identify differences in the progress of the effect of institutional changes and organizational transformation in Indonesian higher education. The structuration analysis shows that examining the conditions that have resulted in the replication and modification of social systems is the focus of the structuration analysis. The image of structuration theory conveys both a sense of regularity and continuity, as well as respect for the labor that must be done daily and the mundane but essential tasks that must be completed. The finding of this study is that with the mandate that universities have been given to implement the three primary pillars that support Indonesia’s higher education system, the difficulty level of the problem facing Indonesia’s higher education system has increased. We suggest a future research agenda and highlight the changes and transformations in power, interests, and alliances that affect the evolution of higher education institutions.