This study investigates a retrofitting methodology for a critical facility in Sant’Agapito, Italy, characterized by irregular foundations on two distinct elevations that amplify dynamic asymmetries, torsional effects, and soil-structure interactions (SSI) during seismic events. The research integrates accelerometer-derived dynamic assessments with a retrofitting strategy based on elastomeric base isolators. Accelerometer data from ambient and forced vibration tests informed the calibration of numerical models, revealing torsional coupling and differential displacements under simulated ground motions. The proposed intervention employs low-damping elastomeric isolators, strategically installed at the interface between the multi-level foundations and superstructure, to decouple the building from seismic inputs while preserving its architectural integrity.