Numerous and extensive ‘Stone Walled Sites’ have been identified in southern African Iron Age landscapes. Appearing from around 1200 CE, and showing considerable variability in size and form, these settlements are named after the dry-stone wall structures that characterize them. Stone Walled Sites were occupied by various Bantu-speaking agropastoral communities. In this paper we test the use of pXRF (portable X-ray fluorescence analysis) to generate a ‘supplementary’ archaeological record where evident stratigraphy is lacking, survey conditions may be uneven, and excavations limited, due to the overall site size. We propose herein the application of portable X-ray fluorescence analysis (pXRF) coupled with multivariate exploratory analysis and geostatistical modelling at Seoke, a southern African SWS of historical age (18th century CE). The aim of the paper is twofold: to explore the potential of the application of a low cost, quick, and minimally invasive technique to detect chemical markers in anthropogenic sediments from a Stone Walled Site, and to propose a way to analyse the results in order to improve our understanding of the use of space at non-generalized scales in such sites.