The organisation and use of space in domestic contexts remain challenging areas of investigation for archaeology due to the complexity and range of site formation and post-depositional processes. In tropical environments, soil processes speed up the degradation of archaeological and environmental records, and relatively ephemeral structures built of mud or clay degrade quickly after abandonment, leaving almost no traces of human activities behind. This paper presents the results of bulk soil and chemical analyses, artefact distribution, and phytolith analysis from the excavation of a daub house at the early medieval site of Unguja Ukuu (c. 7th–14th c. AD), Zanzibar. High-resolution, systematic sampling for microscopic and elemental analyses proved effective in detecting spatial variability in relatively small areas. However, soil chemical enrichment (e.g. Ca, Mg, Mn, P) usually linked to anthropogenic impact on archaeological deposits appears hardly visible in the Unguja Ukuu house deposits. Instead, measurements of a wider range of elements, including trace and rare earth elements (REEs) proved to be important for detecting elemental signatures related to human activities. Contextual sampling of artefacts and phytoliths were crucial to identify sources of chemical enrichment and, thus, build a picture of spatial organisation within the house. The combined multi-scalar sampling strategy with a multi-proxy analytical approach enabled us to define the layout of the daub structure, indoor/outdoor spaces and activity hot-spots. Although macroscopic traces of past activities were almost completely obliterated, archaeological remains of earthen architecture and the use of space can be detected even in such complex tropical settings.