Post-glacial schematic rock paintings extend across the Iberian Peninsula to the Italian Piedmont. The Rocher du Château is one of the few Alpine sites with such painted figurations, located on a main transalpine route at 1750 m.a.s.l. in the Vallée de la Maurienne (Savoie, France). Archeological excavations in front of the painted panels revealed pigments and pigmented pebbles in archaeological levels attributed to the Neolithic Square Mouthed Pottery culture (SMP culture, 4600-4000 BC). The coexistence of pigments from archeological soils and rock paintings is rare in European prehistory and exceptional for the Neolithic period. The integrated study of these materials, barely attempted before, combined non-invasive in situ methods (digital microscopy and Raman spectroscopy) and analytical studies of micro-samples (SEM-EDX, XRD). The weathering process on the rock surface before and after the layer of paint was studied, and the mineralogical identification of the pigments was analyzed. Complementary physico-chemical analyses were conducted at several scales of observation to identify the composition of the excavated pigments and pigmented materials. Some of them proved to be anthropogenic blends combining hematite and charcoal of plant origin. This association has never before been identified in other prehistoric European archeological sites. Based on these data, the potential links between the pebbles, the production of pigments, and the rock paintings are discussed.