This study analyzes the restitution process of the Sümela Monastery, located in the Maçka district of Trabzon, within the framework of documenting and interpreting multilayered heritage. The monastery’s architectural evolution from the Byzantine to the Ottoman and Republican periods is examined through its spatial dialogue with the topography, revealing restitution as not merely a formal reconstruction but as a process of knowledge production and representation. The research follows the methodological logic of Letellier and Eppich’s decision-making matrix model, integrating documentation, analysis, and interpretation in a multidisciplinary sequence. Based on extensive architectural surveys, material studies, and comparative analyses, six successive construction and transformation phases were identified. Each phase reflects a different synthesis of structural continuity, material innovation, and symbolic meaning, thereby illustrating the epistemic continuity of the site. The findings demonstrate that Sümela represents a “palimpsest architecture” where physical, documentary, and sociocultural layers coexist without erasing one another. By emphasizing the ethical and cognitive dimensions of restitution, the study reframes conservation as an interpretive act that mediates between historical accuracy and conceptual integrity. Comparative analysis with other Eastern Mediterranean rock monasteries—such as Meteora, Athos, Hosios Loukas, and Panagia Hozoviotissa—further clarifies Sümela’s unique spatial identity formed through its concave relationship with the mountain mass. Ultimately, the study proposes an epistemological restitution model grounded in transparency, reversibility, and interpretive coherence, suggesting that conservation should not only preserve material authenticity but also sustain the evolving meanings accumulated over time within the cultural landscape.