Soil is spatially heterogeneous and needs site-specific management. However, soil nutrient information at larger scale in most cases is lacking. Consequently, fertilizer advisory services become dependent upon blanket recommendation approach. Subsequently, it affects yield and profitability. This study is aimed at explaining soil fertility heterogeneity in Wolaita zone, Southern Ethiopia. About 789 soil samples were collected to evaluate soil physical (color, particle size, and bulk density) and chemical properties (pH, OC, N, P, K, Ca, Mg, B, Cu, Fe, Mn, Zn, PBS, and CEC). The laser diffraction method for soil particles and mid-infrared diffused reflectance (MIR) spectral analysis for OC, TN, and CEC determination were employed. Mehlich-III extraction and inductively coupled plasma (ICP) spectrometer measurement were used for the remaining elements. The result based on principal component analysis showed that 52% of the total variations were explained by exchangeable bases, CEC, pH, available P, Cu, B, and particle sizes. Clay texture and acidic soil reaction are dominant. Soil parameters with the following ranges were found at low status: soil OC (0.2–6.9%), total N (0.01–0.7%), available P (0.1–238 mg/kg), S (4–30 mg/kg), B (0.01–6.9 mg/kg), and Cu (0.01–5.0 mg/kg). Besides, low levels of exchangeable Ca, Mg, and K (Mg-induced K deficiency) on 22, 34, and 54% soil samples, respectively, were recorded. The soil contained sufficient Fe, Zn, and Mn. In conclusion, the study aids in developing practical decision for optimum soil management interventions and overcomes lower productivity occurring due to fertilizer use that is not tailored to the local conditions. Overall, continuous cropping, low return of crop residues, and low and/or no fertilizer application might have caused the low status of N, P, K, S, B, and Cu. Therefore, application of inorganic fertilizers specific to the site, lime in acidic soils, and organic fertilizers are recommended to restore the soil fertility and improve crop productivity.