Topography and fertility management practices are critical when examining distribution of spatial heterogeneity of soil properties. The study was carried out on a 52-ha land with undulating topography of a village in Northern Malawi to analyze spatial soil heterogeneity with attention to topography and soil fertility management practices in 2021. The spatial heterogeneity of 12 soil chemical properties and soil texture were examined using geostatistical analysis. At 0–20 cm depth, 115 geocoded surface soil samples were collected. Remotely sensed images were captured using an unmanned aerial vehicle, processed, and analyzed to generate and visualize topographic data. Soil fertility management practices were described using field observations and questionnaire survey. The geostatistical analysis revealed spatial heterogeneity of most soil properties at a scale of 80–650 m. The spatial structure of soil pH, available phosphorus (P), total carbon (TC), total nitrogen (TN), and clay showed strong spatial autocorrelation (Q value <0.25). Calcium (Ca2+) and potassium (K+) had moderate spatial autocorrelations (Q values >0.25–< 0.75), whereas magnesium (Mg2+), sodium (Na+), sand, and silt had weak spatial autocorrelations (Q value >0.75). The spatial heterogeneity in TC, K+, Mg2+, CEC, clay, silt, and sand was influenced by the area's topography, whereas pH, P, TN, and Ca2+ were influenced by soil fertility management practices. While change can be negative or positive, differences in topography and fertility management practices significantly changed the physicochemical soil properties, and consequently affected their distribution. TN and P increased with the application of fertilizer, and manure, respectively. Increase in elevation and slope induced positive changes in CEC, K+, Mg2+ and clay. These results could be helpful in the development and application of precision agriculture in the village.