The intellectual Muslim community is living in a dichotomy between faith and science. On the one hand, Islamic teaching tells us that knowledge brings us closer to God and substantiates our faith with rational evidence. On the other hand, the predominant western culture in the modern scientific community rejects the notion of believing in the unseen and sidelines it under the topic of metaphysics, with all the negative connotations associated with it. As a result, the path of living according to faith and the path of scientific investigation diverged further from each other, seemingly with no point of convergence. This article is aimed at removing the obstacles erected by the empiricist outlook in the scientific methodologies, which hinders the integration of religious knowledge and scientific output in a unified framework. Our discussion on the scientific methodologies from the Islamic perspective shows that rational and empirical faculties can be utilised to their fullest potential in a complementary manner. Emerging from the understanding that religion and science are the two valuable engines of human civilisation, an ideology based approach for the study of natural systems can be adopted. In this part of the article, the tenets of empiricism and Karl Popper’s notion of falsification are contrasted with the Islamic concept of certainty (yaqÄ«n).