Santa Maria de Alcobaça Monastery, a Cistercian monastery, was established in 1153, in the year of St. Bernard of Clairvaux’s death. From the approximately 160 illuminated manuscripts produced during the late 12th to early 13th centuries, a set of 15 manuscripts was selected to characterize the medieval colour palette of this scriptorium, following an interdisciplinary study on Portuguese medieval illumination. Colour paints were fully characterized by Raman microscopy (RM), alongside m-Fourier Transform Infrared Spectroscopy and m-Energy dispersive X-ray fluorescence. The Alcobaça collection shows consistently the use of pink and grey paints, mostly achieved by mixing vermilion and/or an organic red, or a carbon-based black pigment with lead white, respectively. Lazurite was the chosen pigment for blue, being ubiquitous in the studied collection. Azurite was found in the lettering of only one manuscript (Alc. 433). Green is defined as bottle green, commonly seen in Portuguese medieval manuscripts, evidencing the loss of cohesion and adhesion to the support. RM and m-Fourier Transform Infrared Spectroscopy identify a copper complex with a protein, possibly verdigris based. The remaining colour palette comprises orpiment, red lead and two organic dyes (with yellow and dark red) not yet characterised. Darkening is observed for lead white in two manuscripts (Alc. 249 and Alc. 446). RM shows galena, a lead sulfide, as the degradation product of lead white, and a band at approximately 810 cm1, indicating the presence of an arsenatebased species. On Alc. 446, an intense broad band at approximately 339 cm1 was also identified, most likely due to an orpiment- based solid phase in agreement with the reduction of orpiment or the arsenate-based species. A set of experiments was designed to assess the influence of orpiment on lead white degradation, corroborating the previous results and indicating the appearance of a new lead carbonate phase.