Identifying a painting’s pigment palette is crucial for comprehending the author’s technique, as well as for evaluating the degradation of the materials. This paper investigates the stratigraphy and pigments distribution of a 16th-century painting from the Uffizi Galleries collection. Firstly, we obtained compositional information through the cross-sectional analysis of samples using scanning electron microscopy. Secondly, we performed elemental mapping using macro-X-ray fluorescence followed by reflectance imaging spectroscopy. The painting image cube was analysed using the spectral correlation mapping (SCM) classification algorithm to accurately identify the distribution and composition of the pigment mixtures.