The settlement of Ust-Voikar is one of the unique multilayered archaeological sites of north-west Siberia. The settlement was inhabited in the late Middle Ages and the early modern period by the Ob Ugrian or northern Khanty ethnographic group. Due to the presence of a frozen cultural layer ruins of wooden residential buildings and other organic materials are well preserved. Plant macroremain, pollen and non-pollen palynomorph (NPP) analyses were applied to samples of the cultural layer from different parts of buildings and from space between them to establish the vegetation cover, plants used by the population, and differences between functional zones in the buildings. For the first time, the NPP analysis combined with statistical methods were used to clarify the settlement planning and human economic activity. Plant communities around the Ust-Voikar settlement were typical for the northern taiga subzone, some settlement's areas were overgrown with weed vegetation. Residents did not engage in agriculture and used local plant resources for construction, medicinal and food purposes. According to macroremain and NPP data were reconstructed (i) the use of spruce branches and cereal bedding indoors and outdoors on wet sites; (ii) the careful use of fire indoors; (iii) the presence of animals indoors; and (iv) whipworm infection. The cluster analysis and principal component analysis of NPPs helped to clarify the planning affiliations of several samples with the unclear origin and to suggest ways in which archaeological objects were used by the inhabitants.