Excavations conducted between 2010 and 2012 at Magoro Hill, a site in South Africa’s Limpopo Province frequented or intermittently occupied by African farming communities since the first millennium AD, yielded a substantial glass bead assemblage. A selection of the beads was studied non-destructively by classifying them according to morphological attributes, supplemented by Raman analyses and XRF measurements. It became evident that a morphological classification of beads recovered from sites that include imports into Africa after the seventeenth century AD could be problematic due to apparent morphological similarities between earlier and later beads. This paper demonstrates the use and archaeological application of Raman and XRF measurements to separate earlier imported beads from later counterparts by identifying glass nanostructure, as well as pigments and opacifiers, which were not used in bead series pre-dating the seventeenth century AD. Results obtained from Raman and XRF measurements indicate that although some beads retrieved from Magoro Hill pre-date the seventeenth century and belong to the Indo-Pacific (K2, East Coast, Khami) and Zimbabwe series, the largest number of beads is from a later European origin. This ties in with the settlement history of the site, which suggests that it primarily served as a rendezvous for episodic rainmaking rituals before it became the stronghold and capital of a Venda chiefdom, headed by the Magoro dynasty, in the second half of the eighteenth century AD. The comparative analysis of the long bead sequence sheds new light on changing patterns in the availability, range, consumption and origin of glass trade beads imported into the northern interior of South Africa over a period of about 1000 years.Graphical abstractGRAPHICAL ABSTRACT CAPTION