Higher education in Europe has undergone remarkable transformations over the last two decades. Germany is a very interesting case in point here. While the country was labeled as a laggard in the process, over the last decade the pace of higher education reforms in Germany has grown considerably. This paper will focus on the by now visible effects of these remarkable transformations, which have led to numerous consequences that go beyond the explicit intentions of policy-makers. Unintended consequences resulting from rapid institutional change will be discussed with regard to research, third-mission activities, and structural reforms concerning governance and organization. It can be assumed that, due to a variety of such unintended consequences, also in other European countries the next decade will be shaped by efforts aiming at reforming the reforms, re-regulating the significant changes brought about during the last two decades. The paper closes with a brief discussion of the necessary linkages to three related interdisciplinary research areas, from which both higher education research and policy-making will benefit, and a summary of the main points of the paper.