The purpose of this paper is to identify an efficient, sustainable, and “green” approach to address the challenges of the preservation of hypogeum heritage, focusing on the problem of moisture, a recurring cause of degradation in porous materials, especially in catacombs. Conventional and novel technologies have been used to address this issue with a completely non-destructive approach. The article provides a multidisciplinary investigation making use of advanced technologies and analysis to quantify the extent and distribution of water infiltration in masonry before damage starts to be visible or irreversibly causes damage. Four different technologies, namely Portable Nuclear Magnetic Resonance (NMR), Audio Frequency–Acoustic Imaging (AF–AI), Laser-Induced Fluorescence (LIF), Infrared Thermography (IRT), and 3D Laser Scanning (RGB-ITR), were applied in the Priscilla catacombs in Rome (Italy). These imaging techniques allow the characterisation of the deterioration of painted surfaces within the delicate environment of the Greek chapel in the Priscilla catacombs. The resulting high-detailed 3D coloured model allowed for easily referencing the data collected by the other techniques aimed also at the study of the potential presence of salt efflorescence and/or microorganisms. The results supply an efficient and sustainable tool aimed at cultural heritage conservation but also at the creation of digital documentation obtained with green methodologies for a wider sharing, ensuring its preservation for future generations.