The São Bento da Vitória Church, a National Monument of Portugal, brings many challenges in evaluating its structural behavior. This research aims to study the structure and systematically collect essential data while considering recommendations for necessary interventions. The building was subjected to a thorough visual inspection, and several cracks were identified. These cracks may be due to settlement issues in the chapel or an out-of-plane mechanism impacting the facade. To investigate this, a series of non-destructive tests (NDT) and numerical analyses were conducted. First, sonic and Schmidt hammer tests, along with the Mechanical Quality Index (MQI), were used to evaluate the mechanical properties of the stone masonry. Additionally, Borescope camera and Georadar tests were utilized to determine the internal characteristics of the walls. To monitor ongoing conditions, crack meters, along with temperature and humidity sensors, were placed. To gain a comprehensive understanding of the building's deterioration, an extensive damage survey was performed. This survey identified the extent of the damage and provided insights into the potential causes. A geometric survey was conducted using both traditional methods and modern techniques such as photogrammetry to complement this. With detailed information on the building's geometry, material properties, and the extent of deterioration, assumptions were made for Finite Element Modeling (FEM) using DIANA software. Pushover analyses indicated that the structure is safe in a seismic occurrence, a reassuring conclusion given the church's location in northern Portugal. However, uncertainties remain. Further investigations, proposed repairs, and a comprehensive maintenance plan are recommended.