Non-destructive analysis of the artist’s palette of ancient wooden panel paintings is a difficult task and studies are rare. Here we compare different methods of analysis of a wooden panel painting, dated to the early sixteenth century, mainly by Raman and infrared spectroscopies. Raman spectra were recorded on collected/sampled micrometric fragments using portable Raman instruments with laser excitation lines at 532 and 785 nm and transportable Raman instruments at 532, 633 and 785 nm; a fixed 1064 nm Raman spectrometer was also used. Infrared analyses were performed in Attenuated Total Reflection (ATR-FTIR) mode. Using the portable instrument, the Raman spectra evidenced white lead, calcite and vermilion only. Raman spectra recorded by transportable and fixed instruments enabled the identification of most of the artist’s palette: (i) white lead, calcite, gypsum and cerussite for white colour; (ii) vermilion, red lead, litharge, haematite for red; (iii) azurite, indigo and lapis lazuli for blue. IR spectra gave information on the organic binding media. XRF analysis on a brown pigment suggested an heterogeneous mixture of a red pigment (such as haematite and/or minium) and a green one as malachite. GC-MS analysis allowed identifying terpenic resin in the composition of the outer protective layer.