Museu Nacional Soares dos Reis (Oporto) owns a pair of Japanese folding screens belonging to the early seventeenth century-Namban genre. As the pieces manifested structural conservation issues, they were subjected to an intervention between 2000 and 2002 in the National Research Institute for Cultural Properties in Tokyo. According to the restoration report, an unknown substance had been applied to the overall surface, adding a glossy finish, as well as some colors inconsistent with the original painting. These materials seem to correspond to a restoration work conducted in the Western countries, but this intervention appears neither in the museum records nor in other historical sources. The aim of this work is to determine the materials used in this restoration work of which very little is known and to understand why these new materials appear in a worse condition of preservation than some of the original ones. Preliminary, in situ, Energy Dispersive X-ray Fluorescence analyses were performed, and right from the beginning, elements such as Cr, Ba, and Co appear in the spectra of orange, yellow, brown, and blue areas, accusing the anachronism of the used materials. Nineteen microsamples were collected to be analyzed with two different confocal Raman equipments using 514, 532, 638, and 785-nm laser sources. Interesting results were obtained for the blue decoration of one of the houses: whereas the energy dispersive X-ray fluorescence spectrum showed the odd combination of Cr, Fe, Co, Cu, and Zn, the Raman spectra indicated mostly the use of Phthalocyanine blue.