This work focuses on the 9th century methodological conflict between John Scot Eriugena and his opponents Prudentius of Troyes and Florus of Lyon, and it discusses the principles and applications of their methodologies. Analysis of Eriugena''s treatise De praedestinatione shows that he bases his exegesis on the rules of philosophy, because according to him a philosophical truth coincides with the Truth of faith. Examination of the writings of Eriugena''s opponents - Prudentius and Florus - demonstrates their attempts to distinguish between truths of philosophy and the Truth of theology and, consequently, between philosophical and theological methods. In spite of that, as this work shows, Eriugena''s opponents themselves could not avoid applications of dialectical tools in their refutations of his theses. For those who are interested in the early medieval philosophy.