The preservation of the Athenian Acropolis monuments constitutes an ongoing top-priority national project of global significance and impact. The project concerning the analytical investigation of the polychromy of the Acropolis monuments presented in this paper was part of the Acropolis Restoration Service (YSMA) program (2011–2015), regarding the restoration of the two corners of the west entablature of the Parthenon, which exhibited severe static damage, and a parallel restoration program of the Propylaea. The scope of this research was to investigate the materials in the paint decoration remains on the monuments by applying, entirely in situ, numerous non-invasive techniques on selected architectural members of the Parthenon and the Propylaea. The research focused, mainly, on surfaces where traces of colour or decoration patterns were visible to the naked eye. Furthermore, surfaces that are referred to in the literature as decorated but that are currently covered with weathering crusts (of white or black colour) and/or layers of patina (of yellowish and orange-brown hue), were also examined. The techniques applied in situ on the Acropolis monuments were X-ray fluorescence, micro-Raman, and Fourier Transform InfraRed (FTIR) spectroscopic techniques, conducted with the use of handheld or portable instruments. The scientific data gathered in situ are discussed in this paper to enhance our knowledge of the architectural polychromy of the classical period. Further investigation by applying analytical techniques on a few selected micro-samples would be highly complementary to this present work.