Fifty-four pieces out of 356 marble pieces deriving from the decorative and architectonic apparatus of the medieval monastic complex of S. Francesco of Castelletto (Genoa, Italy) preserve traces of varicolored paint layers. Microscopic samples of green, blue, red, pink, white, and yellow paint relics were collected by scalpel and analyzed by means of Scanning Electron Microscope coupled with Energy Dispersive Spectroscopy (SEM-EDS), µ-Raman, and Fourier Transform Infra-Red Spectroscopy with Attenuated Total Reflection (FTIR-ATR), to characterize pigments and binders. The combined results from the different techniques allowed verification that stone decoration in Genoa during the Middle Ages encompassed a calcite groundwork and the use of a mixture of oils and proteins (probably egg) to apply pigments. The assemblage of impurities within the pigment has been correlated with the provenance sites along the commercial continental (Hungary and France) and maritime (Sardinia, Cyprus, or Veneto) routes between the 13th and 15th centuries. Moreover, the investigation of the painted layer improved the characterization of the decorative techniques in use in Genoa during the Middle Ages.