The declared objectives of the state education policy in Russia are education quality improvement and cost optimization. Higher education reform refers to a long-range effort, and it may take at least 10 years to reap the fruits. High-quality and affordable higher education is among the necessary factors which are responsible for regional economic development. Institutional complementarity refers to situations when existing institutions have a reinforcement effect on the ongoing institutional change, thereby generating coherent and stable structures. The Russian experience of transformation shows orientation toward the mergers of essentially identical higher educational institutions, which are state-owned organizations with vertical management structures. Institutional changes that occur in the reorganized university should correspond to the general agenda of the Russian higher education system development. In other words, their key points have to be complementary to each other. However, being implemented, higher education reforms often result in institutional and organizational change that do not comply with due understanding of reforms as a systematic process. This paper adopts a research framework of original institutional economics to identify relevant institutional changes which occur in the process of academic reorganization – i.e., establishment of the Federal Universities and «Flagship» Universities in the South Federal District, Russian Federation. In-depth interviews with the representatives of reorganized universities have been conducted to assess the degree of complementarity between the institutional change and management routines, from the one hand, and to discuss whether the implemented reforms are systemic as such, from the other hand. Research findings suggest that existing incentives and system of motivation are distorted; technological and relational routines are either destroyed, or increasingly complicated; ongoing centralization and bureaucratic sprawl within the universities result in increased transaction costs. Evolutionary changes in organizational routines may reduce transaction costs as such; however, prescriptive character of ongoing institutional reforms in the reorganized institutions of higher education destabilize informal group beneficial institutions, or even prevent their emergence.