The Carrer Paris site is located in Cerdanyola del Vallès (Barcelona, Spain). It is a Chalcolithic hypogeum dated between 3800-4100 BP with more than 60 individuals distributed in four burial levels. We study the remains of Individual 5 from burial level II. It is an adult skeleton, preserved in anatomical position and buried with Campaniform pottery. During the excavation, we identified red pigment on the mandibular symphysis region of the individual 5. In this work we present the preservation state and conservation methodology to restore the individual 5 cranium and mandible. At the same time, we present the results of the pigment composition analyzed by non-destructive methods. These analyses were conducted directly on the pigments and the bone surface with environment electronic microscopy (ESEM-EDS) X-ray micro-diffraction (µ-DRX) before the conservation treatments. The objective of the analysis was to characterize the pigments, the bone and the clays to apply the best methodology to conserve the pieces. The combination of both techniques allows us to analyze the area of interest without removing samples. These analyses were performed directly, without affecting the bone and pigments and assuring the integral preservation of the objects. The results reach us new data on the use of pigment in funerary rituals during the Chalcolithic.