The mission of Higher Education Institutions (HEIs) has progressively developed from an educational role to knowledge production, innovation generation and engagement with society at large. At the same time, the HEIs space has been enriched with the evolution of ‘non-university’ institutions, and a clear drift between the university and ‘non-university’ sectors can be observed all over the world. This challenges current higher education (HE) non-unitary systems and questions the validity of criteria currently used to typify HEIs. This study was initiated to clarify the status of the HE divide in European countries, by assessing the research characteristics and performance of several HEIs. To this end, HEIs in France, Italy and Portugal were analyzed using a multi-dimensional set of quantitative and qualitative indicators. It can be observed that in Portugal the HE drift is both policy and practice driven. The evidence and conclusions of this study can be considered by policy makers when developing public strategies and policies aimed at the ‘non-university’ sector in contemporary research and innovation ecosystems.