The data presented in this article derives from archaeological cremated bones excavated in 2014–2015 at Aakre Kivivare tarand cemetery, S Estonia. The material covers bone fragments of different colours to be assessed visually, using Video Spectral Comparator (VSC) and analysed comparatively with Fourier Transform Infrared Spectroscopy (FTIR) to determine the structural and compositional changes in the thermally altered bone and implications of the latter in bone colouring. The dataset comprises FTIR spectra measurements, colour spectra measured with VSC and visually assessed colour of human and animal bones chosen for the study. This dataset is expected to be a comparative source for determining archaeological cremated bone colour induced by heat-related changes in the bone microstructure, supporting the visual estimations of temperature-based cremation practices in archaeological and forensic bone material in the future