Philip Melanchthon transformed the natural philosophy which was traditionally taught by the Schoolmen at universities into a Lutheran one. The late medieval Schoolmen frequently commented upon Aristotle's books on nature with the quaestio method and appealed to the authority of Aristotle, the Schoolmen and the Church. As part of university learning, natural philosophy contributed towards knowledge of God and alongside metaphysics it was an essential area of knowledge for theologians. The system of thought of the Schoolmen, tightly knit together by means of logic, was ultimately based on a conviction that rational knowledge about God was possible and necessary. Hence natural philosophical arguments were legitimately used to prove, elucidate and maintain theological points.

In contrast, Luther denied the validity of human rational knowledge as a support for theology. Human reason on its own could not affirm theological truths. Natural philosophy of the late medieval Schoolmen was therefore rejected by Luther and Melanchthon – it could not teach the message of the Gospel. Instead, Melanchthon's natural philosophy was knowledge of Law in the sense that it provided the theoretical foundation of his moral philosophy of civil obedience.