Agricultural land degradation due to nutrient deficiencies is a threat to agricultural sustainability. As nutrients availability is influenced by soil heterogeneity, climatic conditions and anthropogenic activities; hence, delineation of nutrient management zones (MZs) based on spatial variability could be an effective management option at regional scale. Thus, the present study was carried out to delineate MZs in the Shiwalik Himalayan region of India by capturing spatial variability of soil properties and secondary and micronutrients status because of the emerging nutrient deficiencies. For the study, a total of 2575 geo‐referenced representative surface (0–15 cm depth) soil samples were collected from the study region covering an area of 53,483 km2. The soils were analysed for pH, electrical conductivity, soil organic carbon, available sulphur (S) and micronutrients (Zn, Fe, Cu, Mn, B and Mo) concentrations. There was a wide variation in soil properties with coefficient of variation values of 14 (for pH) to 86% for available Mo. Geostatistical analysis revealed spherical, Gaussian, exponential, stable, circular and K‐Bessel best‐fit models for soil properties. Most of the soil properties were having moderate spatial dependence except soil pH and S (strong spatial dependence) and Zn (weak spatial dependence). About 49%, 10%, 2%, 13%, 11%, 12% and 8% area of the study region were found to be deficient (including acute and marginal deficiency) in S, Zn, Fe, Cu, Mn, B and Mo, respectively. The principal component analysis and fuzzy c‐mean clustering were performed to develop the MZs. Four principal components with eigenvalues greater than 1 and accounting 65·4% of total variance were retained for further analysis. On the basis of fuzzy performance index and normalized classification entropy, four potential MZs were identified. Analysis of variance confirmed the heterogeneity in most of the studied soil properties among the MZs. The study indicated that the methodology of delineating MZs can be effectively used in site‐specific S and micronutrients management in the Shiwalik Himalayan region of India. Copyright © 2016 John Wiley & Sons, Ltd.