This paper parallels the changes experienced by universities and science at the beginning of the new century in order to explore one relevant source of resilience and change inside the universities’ institutional fabric, which is its persistent dependence on the signs and norms produced by science as a nested institution. In no small degree, science is organized according to its norms and values. Notwithstanding, it de facto exists inside the institutional environment created by the university. As such, one could argue that it is a nested institution. Our argument holds that the interplay between the institutional norms coming from the university and science gives rise to one of the more relevant sources of resilience of universities. The paper explores the soundness of these assumptions on primary data collected in a research focusing on the responses of lower-level academic unit leaders in two universities: the University of Tampere, Finland, and the University of São Paulo, Brazil. In each case, we explore the local responses to the changes engendered by autonomy as a proxy of the substantial change in the university's environment, to map how the small academic units respond to a quickly changing external environment.