Thomas Kuhn’s model of paradigm shift as an intra-systemic framework to account for changes within the scientific discourse has been adopted by scholars in different fields as diverse as sociology, theology, economy, and education, to name only a few. The present study argues that the same model can usefully be drawn upon to examine the relationship between ‘science’ and ‘religion’ with some reservations during the Renaissance. To further illustrate the interconnection, the study focuses on Francis Bacon’s utopian text New Atlantis and shows the way the author is attempting to emphasize the symbiotic co-existence of the two paradigms in an ideal society. However, viewing the work within a larger context, one can see how Bacon’s text seems to be an intermediary link between the Church- and science-controlled discourses. The study also shows that although towards the end of the Renaissance, the scientific paradigm gains in popularity, the religious discourse is also present and makes its presence strongly felt.