ABSTRACT In-field variability of soil properties creates niches that have been perceived by smallholder farmers, especially in hostile environments, as constituting an essential part of their subsistence farming. They can exploit niche variability as a risk minimisation strategy for crop production. Smallholder farmers largely base their nutrient management strategies on their perception of niche fertility. The study physically and chemically characterised soil samples up to the 130 cm depth of predominant arable niches from a representative sample of nine smallholder farms with fields cropped for over 70 years. The niches were homestead surroundings, termitaria environments, areas under Parinari curatellifolia and open sandy patches. The data were analysed using discriminant analysis, a statistical method that investigated niche differentiation based on simultaneous analysis of soil nutrient variables. The analysis of variance complemented the discriminant analysis. Results showed that the first two discriminant functions contributed significantly (p < 0.001) to niche differences and accounted for 95% of the total variation. The discrimination was most powerful in classifying termitaria environments and around homestead niches, indicated by greater than 81% aggregation of cases. Termitaria environments had the lowest significant (p < 0.05) bulk density of 1.47 g/cm3 while the remaining niches had bulk densities greater than 1.57 g/cm3. The texture of termitaria environments significantly differed (p < 0.001) from the rest of the niches and consisted of sandy loams and loamy sands. Homestead surroundings, areas under P. curatellifolia and open sandy patches had sandy soils with greater than 90% sand. Macronutrients generally declined with depth. Total C in the 0–20 cm was relatively high in under P. curatellifolia (14.8 Mg/ha) and lowest in the open sandy patches (7.2 Mg/ha). Total N for all niches was low (<1.4 Mg/ha), indicating possible limitation to crop growth. Available P in the active rooting zone of 0–40 cm was adequate only in homestead surroundings (30–50 ppm) and marginal (15–30 ppm) in termitaria environments and under P. curatellifolia. However, it was deficient in the open sandy patches. Homestead surroundings and termitaria environments were the niches with relatively high soil pH (>6.5) and exchangeable base content of Ca, Mg and K. Areas under P. curatellifolia, perceived by farmers to be more fertile, had no comparative advantage over the open sandy patches in texture and macronutrient levels. Farm management practices of applying less nutrient inputs to termitaria environments and areas under P. curatellifolia were misguided and perpetuated low productivity in smallholder cropping environments. We recommend site-specific nutrient management of niches where limited purchased nutrients are applied to relatively fertile niches, for example, homestead surroundings and termitaria environments while open sandy patches are left to recover under natural or improved fallow.