Much has already been written about the relationship between science and religion. In the Iberian context, however, religious houses, viewed as an important site for fostering scientific practices, are a topic that still requires closer scrutiny. The main purpose of this paper is to show the importance of the Portuguese religious houses in the context of Iberian Science in Early Modern world, through the study of former religious libraries and their scientific content. In Portugal’s archives and libraries, the number of scientific books with inscriptions of provenance from former religious libraries is impressive. This paper tries to show that the religious houses were not just the most important repository of scientific books in Portugal, but also a site of scientific activity. This paper is part of a larger current research project on the acquisition and circulation of scientific books in Portugal in the 15th-18th centuries. This project attempts to reconstruct the scientific collections of the former monastic libraries on the basis of their historical catalogues. These huge collections were totally dispersed after the waves of secularisation of the 18th-19th centuries. By exploring the extant library catalogues and inventories of the major religious orders it is possible to identify a rich corpus of texts which enlightens the diffusion and the impact of scientific books in Portugal. Library catalogues provide an essential source of information, but an examination of the exemplars is also necessary to reconstruct reading practices. The fruition of scientific books in religious context is considered also in an effort to stress its importance in relation to the scientific practices of each of the different Portuguese religious congregations.