Regional innovation policy is determined by different rationales and philosophies at numerous governance levels. Whether it can unfold its full potential, relies inter alia upon the degree of regional autonomy. In this contribution, we review the topic of regional autonomy, referring to the most recent theoretical contributions in the innovation systems framework and decentralisation processes by taking a dynamic approach. We analyse transformation processes as regards the state of regional autonomy by proposing a set of indicators for European regions suitable for the operationalisation of regional autonomy. Our findings show a variability across Europe as well as a certain evolution over time. Processes of transformation are mainly triggered by policies on the supra-national level and incorporate a shift in the hierarchical power relationship between the nation state and its regions, a management dimension on the operational level, and a resource dimension by actively leveraging efficiency potentials.