By comparing two distinct settings–Portugal and Finland–and based on previous studies revealing similar trends in both countries, this article analyses the relationship between institutional and academic autonomy in the higher education sector. Based on crosschecking of the literature review and 47 interviews with key actors in both the Portuguese and Finnish higher education systems, the authors analyse the extent to which the political attempts to increase institutional autonomy are perceived by academics in these countries as leading to an increase in their professional autonomy. Data reveals that there is a lack of complete correspondence between the way different institutional dimensions have been changing at the organisational level and the way academics perceive the effects at the professional level. While there is a correspondence in the perceptions over organisational and interventional autonomy, no correspondence is found concerning policy autonomy in both countries. Furthermore, there are no homogeneous perceptions within academics group in each country concerning professional autonomy.