A detailed archaeometric study of a Late Neolithic cup found in the São Paulo Cave, Almada, Portugal, has been made, which, according to its unique decorative characteristics, may have had a ceremonial and symbolic utilization. Other 23 sherds, collected around the cup, dated early and late Chalcolithic periods, have also been studied. The conjugation of the information provided by the Raman, X‐ray diffraction, and X‐ray fluorescence emission experiments for the locally collected cup, sherds, and clays, with emphasis on the analysis of the ceramic bodies, allowed the characterization of the artefacts. In the reddish, brownish, or black parts of the surface of the cup, haematite, magnetite, and carbon black pigments were identified, whereas in the whitish parts, quartz was the most common mineral. Three main groups could be identified in the ceramic bodies, although all were made with the use of locally collected clays. In the first group, where the Neolithic cup is included, the potters used Miocene clays, most probably from the Palença clay sources, which were fired at a high temperature of about 950°C. The second group was also produced with raw materials of Miocene origin but the firing temperature was much lower, around 800°C, as revealed by the existing amount of muscovite. The third group, with clays of a Pliocene origin, exhibited a much lower content of calcium carbonate, as evaluated by the R index ([SiO2 + Al2O3 + K2O]/CaO), considered as ceramic raw material or a geological source indicator. These clays contain high amounts of kaolinite, muscovite, quartz, microcline, and anatase.