This study aims to review Francis Bacon’s role in the secularization of modern science. This subject becomes more significant when we consider that Bacon frequently referred to Holy Scripture. This, however, raises the question of how he can be regarded as one of the most influential figures in the secularization of science. Using a descriptive-analytical approach, this paper shows that several key components of Bacon’s intellectual system had a decisive impact on the secularization of modern science: the rejection of the final cause and the predominance of a mechanical worldview; the shift in the method and goal of science from the discovery of truth to mastery over nature; the critique of Scholastic philosophy and a disregard for abstract analysis, under the pretext of making modern science efficient and productive; and the abandonment of theological discussions due to their perceived lack of influence on production. Each of these principles contributed, in its own way, to distinguishing metaphysical and theological analyses from the new science. Bacon is a founder of empiricism, and his theories led to the consolidation of a worldly view of nature and also served to justify the exploitation of nature and of other human beings. Therefore, despite his frequent citations of the Holy Scripture, his thought unequivocally culminates in the secularization of science. Apart from its unjustified consequences, Bacon’s perspective is marred by serious epistemological flaws.