The paper reports on the exploitation of an educated multi-technique analytical approach based on a wide non invasive step followed by a focused micro-destructive step, aimed at the minimally invasive identification of the pigments decorating the ceiling of the Gilded Vault of the Domus Aurea in Rome. The combination of elemental analysis with molecular characterization provided by X-ray fluorescence and UV-vis spectroscopies, respectively, allowed for the in situ non-invasive identification of a remarkable number of pigments, namely Egyptian blue, green earth, cinnabar, red ochre and an anthraquinonic lake. The study was completed with the Raman analysis of two bulk samples, in particular, SERS measurements allowed for the speciation of the anthraquinonic pigment. Elemental mapping by scanning electron microscopy-energy dispersive spectrometer combined with micro-fluorimetry on cross-section gave an insight into both the distribution of different blend of pigments and on the nature of the inorganic support of the red dye.