This paper examines the development of dogmatics as a theological discipline in the confessional era. With his Loci theologici (1521), Philipp Melanchthon developed a new method of doing theology that became the model for Protestant theology in the era of confessionalization. While his approach focused on explaining the content of the Christian faith, Melchior Cano used the same method in his theological Loci (1543-60) to describe the authorities of theological knowledge in line with the Council of Trent, thereby stimulating the development of epistemological prolegomena in Protestant theology. In the Protestant exposition of the Christian faith in accordance with the principles and insights of the Reformation, philological and exegetical analysis and systematic interpretation were naturally combined. Among the many challenges theology faced, two central demands led to a differentiation of theological disciplines and a growing distinction between biblical studies and systematic theology, which this paper will explore. One was the pressure to establish theology as an academic discipline; the other was the challenge of developing criteria for distinguishing between fundamental and non-fundamental articles of faith. The paper analyses these developments and demonstrates how the Lutheran philosopher and theologian Johann Franz Buddeus (1667-1729) responded to these challenges in the early eighteenth century in his theological encyclopedia and in his definition of dogmatics in distinction from scriptural exegesis.