It is possible to analyse in a systematic manner the evolution of university autonomy and academic freedom in Europe after 1999-2000, a distinct and remarkable period in the history of European higher education. A consistent, albeit surprising, pattern can be identified: it consists of a combination of diverging paths of development. We define the path of development as a distinguishable, cohesive, interconnected and relatively stable sequence of events or changes taking place over a longer period in a given area, which are characterised by a distinctive combination of speed, direction and substance (content). To illustrate briefly, we propose two examples, which we will analyse in this chapter.We argue that there is a difference of direction, speed and content, or different paths of development, in the evolution of institutional autonomy compared to academic freedom: this period shows much faster and mainly progressive changes in autonomy, as opposed to slower and rather regressive changes in academic freedom in Europe, both at the conceptual level and in practice. If we look at autonomy alone, we notice a particular path of development: an accelerating tendency to define, measure and practice it in relation to efficiency, rather than intellectual, moral and legal references, including human rights. We call this the instrumental path of development of autonomy in the EHEA.In this chapter, we attempt to identify the most important paths of development in academic freedom and university autonomy in the EHEA, analyse their interaction and explore their significance for the broader discussion about the present and future of higher education in Europe.