As is well known, the deterioration of wall paintings due to the capillary rise of water through the walls is a very widespread problem. In this paper, a study of microclimate monitoring, unilateral nuclear magnetic resonance (NMR), and evanescent-field dielectrometry (EFD) was applied to map non-destructively, in situ, and in a quantitative way the distribution of the moisture in an ancient deteriorated wall painting of the eleventh century. Both unilateral NMR and EFD are quite new, fully portable, and non-destructive techniques, and their combination is absolutely new. The approach reported here is proposed as a new analytical protocol to afford the problem of mapping, non-destructively, the moisture in a deteriorated wall painting in a hypogeous building such as that of the second level of St. Clement Basilica, Rome (Italy), where the use of IR thermography is impaired due to the environmental conditions, and the gravimetric tests are forbidden due to the preciousness of the artifact. The moisture distribution was mapped at different depths, from the very first layers of the painted film to a depth of 2 cm. It has also been shown how the map obtained in the first layers of the artwork is affected by the environmental conditions typical of a hypogeous building, whereas the maps obtained at higher depths are representative of the moisture due to the capillary rise of water from the ground. The quantitative analysis of the moisture was performed by calibrating NMR and EFD signals with purposely prepared specimens. This study may be applied before and after performing any intervention aimed at restoring and improving the state of conservation of this type of artwork and reducing the dampness or extracting salts (driven by the variation of moisture content) and monitoring the effectiveness of the performed interventions during the time. This protocol is applicable to any type of porous material.