The conservation of culturally stratified heritage structures requires a holistic approach that balances the protection of historical integrity with the integration of contemporary functions. This study focuses on the Aya Payana Church, a late Ottoman rural ecclesiastical structure located in Isparta, Türkiye, as a case study to explore sustainable conservation and adaptive reuse strategies. Although the building retains much of its original physical fabric, its evolving uses—from sacred space to military storage and eventual abandonment—reflect a layered cultural narrative. In line with international conservation charters, intervention strategies were developed based on principles of minimal intervention, reversibility, and respect for historical authenticity. The adaptive reuse strategy involved transforming the site into a sensory-focused cultural facility, featuring a “Kokuhane” (scent museum) and a botanical garden cultivating local aromatic plants. This integration promotes active visitor engagement through laboratory workshops and enhances cultural continuity by linking traditional knowledge with contemporary experience. A transparent cafeteria structure was added with minimal visual impact, ensuring the preservation of the historical silhouette while improving visitor services. The proposed model demonstrates that sustainable conservation of culturally layered sites can be achieved through adaptive reuse strategies that prioritize historical integrity, cultural sustainability, and community engagement. The findings offer a replicable framework for future conservation projects aiming to revitalize underused rural heritage buildings while maintaining their cultural significance.