Higher education institutions in Portugal, as in many developed countries, have undergone deep transformations affecting their organisational structures and professionals. These reforms framed by new public management are said to induce changes in the traditional jurisdictional field of the academic profession with the administrative power being transferred to non-teaching staff. The aim of this paper is to contribute to this discussion by analysing the extent to which the academics jurisdictional field has changed and power relations were redefined. Resorting to empirical data obtained through an extensive online survey we analyse professionals' perceptions on changes in institutional governance and on their professional autonomy and the way this may translate a reconfiguration of power between these professional groups. The empirical findings suggest that professionals perceive changes as affecting negatively their participation in institutions' decision-making processes but this is not automatically translated in a perceived loss of professional autonomy.