The Basilica Cathedral of Lima, situated in the city’s historic center, features a rich collection of carved wooden artworks, paintings, and sculptures spanning Gothic, Renaissance, Baroque, and Plateresque styles. This diverse array of artistic and architectural elements makes it a testament to the city’s historical evolution. This article presents the results of employing a range of non-destructive techniques to document structural pathologies and characterize the cathedral’s structural system. Additionally, it proposes a systematic focused on experimental structural assessment. The results of this assessment will later be incorporated into a Historical Building Information Modeling (HBIM) model, which will be developed throughout the entire process. In this context, the article also addresses the challenges associated with creating digital models from point clouds captured through laser scanning and aerial photogrammetry. While various methods exist for assessing or diagnosing heritage buildings, there is limited research on structures composed of masonry, adobe, quincha, and wood - such as the Basilica Cathedral of Lima, which is in a highly seismic region. The integration of these techniques, guided by the proposed protocol, aims not only to define the current state of the building but also to lay the groundwork for the future development of a digital twin that includes real-time sensing capabilities.