The walls and mural paintings of Pompeii exposed directly to the rainfalls are the most impacted in view of the observed decay. However, there are also wall paintings in protected rooms showing evidences of decaying. The aim of this research was to study the salts formed in such protected wall paintings only by non-invasive and in-situ Raman spectroscopy to understand their decaying processes. The perystile of the House of the Gilded Cupids (Regio VI, Insula 16), one of the most important houses of Pompeii was studied. Although an exhaustive restoration was carried out in 2004, a new conservation treatment was needed in 2013 and only two years later, extensive crystallizations of soluble salts were again threatening several of the restored surfaces, thus, the presence of an unsolved degradation pathway was deduced. Thank to the proposed methodology, it was pointed out that the key is the acidified rainfall impact in the non-protected backside of the walls containing the wall paintings. Thus, a new concept in the preservation of the houses of Pompeii is provided, in which the need of the protection of those walls from both sides is suggested to avoid the movement of water through the pores of the walls.