The pigments, execution technique and repainting used on the polychrome wood ceilings and doors in the Casa de Pilatos (Seville, Spain) were studied using portable X-ray fluorescence equipment. Cross-sections of small samples were also analysed by optical microscopy, SEM with EDX analysis, micro-Raman and micro-infrared spectroscopy and X-ray diffraction. These carpentry works are magnificent examples of the Mudéjar art made in Spain in the early 16th century. Portable X-ray fluorescence gave good information on the different components of the polychrome. The SEM-EDX study of the surfaces of small samples gave information on their components and also characterized the compounds that had been deposited or formed by environmental contamination or by the alteration of some pigments. The SEM-EDX study of cross-sections facilitated the characterization of all layers and pigments from the support to the most external layer. The following pigments were characterized: red (cinnabar/vermillion, lead oxide, iron oxides and orpiment/realgar), black (carbon black), white (white lead and titanium barium white), yellow-orange-red-brown (orpiment/realgar and iron oxides), green (chromium oxide), blue (indigo blue and ultramarine blue), and gilding (gold leaf on bole). False gold, bronze and brass were also found. The pigments were applied with the oil painting technique over a support layer that had been primed with animal glue. This support layer was gypsum in some cases and white lead in others. This study is essential to the polychrome conservation of the studied artwork, and it will help clarify uncertainties in the history and painting of Mudéjar art.