Iranian architecture has historically evolved in close association with spirituality. This relationship is reflected not only in its spatial and physical organization but also in its philosophical and theoretical foundations. Drawing upon Mulla Sadra’s Transcendent Philosophy and the Fourfold Model of Cognition, this study investigates the spiritual dimensions of Iranian architecture. This qualitative study adopts a logical–interpretive approach based on Islamic-Iranian philosophical sources and selected examples of traditional Iranian architecture. The theoretical framework is grounded in Mulla Sadra’s Transcendent Philosophy, which is founded upon the principles of the Primacy of Existence, the Gradation of Existence, and Substantial Motion. From this perspective, architecture is understood not merely as a physical artifact but as an existential phenomenon capable of manifesting these philosophical principles. The Fourfold Model of Cognition, rooted in Iranian philosophical thought and the doctrine of the apparent (ẓāhir) and the hidden (bāṭin), provides an analytical framework for understanding the relationship between architecture and wisdom. The model consists of four interconnected levels—concepts (meanings), foundations (principles), patterns (design frameworks and methods), and exemplars (cases and applications)—through which the reciprocal movement from meaning to matter (the hidden to the apparent) and vice versa is examined. Based on theoretical analysis and field observations of the Sheikh Lotfollah Mosque, the findings demonstrate that, through the principles of Transcendent Philosophy, Iranian architecture extends beyond aesthetic and functional considerations to provide a mystical and ontological experience of space. This perspective offers an understanding that transcends form and function, connecting architecture with spiritual and intuitive dimensions of human experience. The findings suggest that the philosophical foundations of Mulla Sadra’s Transcendent Philosophy can provide a theoretical basis for revitalizing the transcendent dimensions of contemporary architecture. In this regard, the Fourfold Model of Cognition offers a valuable methodological framework for interpreting and designing architectural spaces through a spiritual perspective.