Tracing the origin of glass trade beads excavated at archaeological sites can contribute significantly to dating a site and reconstructing prehistoric trade routes. Wood developed a temporally sensitive bead sequence dating from the 8th to the 16th century AD for beads excavated at southern African sites that is commonly used by archaeologists to classify beads according to their morphology. In this study, we develop a multidisciplinary methodology to refine the classification of glass beads based on morphology alone. Glass trade beads excavated at 11 sites along the upper reaches of the Limpopo River in east-central Botswana are used as case study. The beads were visually classified according to their morphological properties (colour, size, etc.) and analysed with Raman spectroscopy and portable X-ray fluorescence (XRF). Energy Dispersive Spectroscopy (EDS) of one bead showed that two types of glass were sintered together to form a recycled product, explaining the divergence of Raman spectra recorded on different zones. The study confirms the value of a morphological classification based on existing data sets as a first approach, but demonstrates that both Raman and XRF measurements can contribute to a more exact classification of glass beads imported into southern Africa from the East before the 17th century AD.