This article explores underlying mechanisms triggering a change in conceptualization of innovation in the European Union (EU), the impact of this change on institutional demands upon European universities and implications for evaluation procedures. We mobilize the theoretical concept of critical junctures to explore significant periods that have affected understanding of innovation in the EU as well as institutional expectations from universities. Through an analysis of European policy corpus relating to innovation, we identify three distinct periods, 1983-6, 1995-2000, and 2008-12, entailing fairly fundamental shifts that have considerably broadened the understanding of innovation and then demonstrate the way this broadening conceptualization has affected institutional demands upon universities. Following this, we discuss the implications of the critical junctures on evaluation approaches. We conclude by arguing that different approaches towards innovation have created complex institutional environment for universities to navigate and suggest that implementing more nuanced and customized evaluation schemes aligned to the institutional demands of each critical juncture could help addressing this complexity.