<p>Rome embodies over two millennia of urban continuity. Historic churches in the city have undergone extensive transformations, offering valuable insights into the evolution of construction techniques. However, tracing their development proves challenging due to limited early documentation and the complexity of the structures. This study tackles these challenges through a two-phase methodology that combines an in-depth literature review with an integrated 3D survey. Spatial data of the lower basilica were gathered using the Structure from Motion method. The analysis was enhanced by contour mapping, and a digital elevation model was created to assist in interpreting the architectural stratification. The proposed approach facilitates a clearer understanding of the layered historical architecture, despite limited access to certain areas. The Basilica of Saint Chrysogonus serves as a case study for this integrated diagnostic method, demonstrating the effectiveness of combining historical and morphometric data in reconstructing the architectural development of complex heritage sites.</p>