Interpretations of the Quran have always been influenced by philosophical, theological, and mystical frameworks, but systematic and comparative studies of these metaphysical foundations in the Shia and Sunni traditions have been less frequent. The importance of this research stems from the fact that most previous studies have focused on the linguistic, historical, or rhetorical dimensions of interpretation and have not addressed the role of ontological and epistemological foundations; while these foundations guide the interpreter's understanding of the verses and determine the boundaries of interpretation. The main challenge of the research is to reveal the implicit metaphysical assumptions that are woven into the interpretive texts in the form of the concepts of "being," "agent," "knowledge," and "interior," and their disclosure requires an integrated and precise approach to classical works. To respond to this need, the present study has addressed the subject of "metaphysical foundations in the interpretation of the Quran from the perspective of the commentators of the two sects" using a qualitative-analytical documentary method. With the focus on case studies, parts of the characteristic interpretations of each school were used; discourse analysis and a comparative framework led to the extraction and comparison of "unity of existence", "monotheism of actions", "present knowledge" and "esotericism" in Shiite interpretation and "originality of occurrence", "divine predestination", "the validity of transmitted reason" and "limited theoretical mysticism" in Sunni interpretation. The findings show that Shiite commentators, by focusing on existential experience and combining theoretical reason and intuition, discover hidden layers of meaning; however, Sunni commentators, while accepting the necessity of going beyond literal interpretation, center on transmitted reason and limit the field of mysticism to a marginal area. This difference in weighting of epistemological sources makes the semantic structure of verses about divine attributes, revelation, prophecy, and resurrection different.