Ion beam analysis (IBA)- and X-ray fluorescence (XRF)-based techniques have been well adopted in cultural-heritage-related analytical studies covering a wide range of diagnostic role, i.e., from screening purposes up to full quantitative characterization. In this work, a systematic research was carried out towards the identification and evaluation of the advantages and the limitations of laboratory-based (IBA, electron probe microanalyzer) and portable (milli-XRF and micro-XRF) techniques. The study focused on the analysis of an Archaic glass bead collection recently excavated from the city of Thebes (mainland, Greece), in order to suggest an optimized and synergistic analytical methodology for similar studies and to assess the reliability of the quantification procedure of analyses conducted in particular by portable XRF spectrometers. All the employed analytical techniques and methodologies proved efficient to provide in a consistent way characterization of the glass bead composition, with analytical range and sensitivity depending on the particular technique. The obtained compositional data suggest a solid basis for the understanding of the main technological features related to the raw major and minor materials utilized for the manufacture of the Thebian ancient glass bead collection.