Vibrational spectroscopy was applied to study cylindrical engraved bone boxes from the Chalcolithic settlement of Vila Nova de São Pedro (VNSP, Azambuja, Portugal) which has the largest and richest artefact assemblage of Copper Age Western Iberia. The objectives were to reconstitute manufacturing techniques, determine the role of pyrotechnology in the production of cylindrical engraved bone boxes and assess oxygen conditions during burning. Four fragments of cylindrical engraved bone “boxes” from VNSP were used in this research. Anaerobic experimental burn conditions were recreated by using a home-made steel airtight chamber under vacuum. Human bone fragments were burnt at 400–1000 °C for 120–211 min. Fourier-transform infrared spectroscopy analyses were performed on bone powder samples. The resulting spectra and chemometric indices were used as a reference to establish comparisons with the archaeological artefacts. None of these presented spectral features compatible with anaerobic burning. Therefore, aerobic burns were used to achieve the whitish look and were most probably used to attain the darker shade displayed by the artefacts. Artefact manufacturing appears to have relied on bone cutting, bone engraving and maybe polishing, followed by heat treatment. The population from VNSP appears to have been highly specialized in the use of fire to work different raw materials.