Citrus spp. are one of the most important commercial crops with global marketing potential in the world, as in Iran. A soil management zone (MZ) as an appropriate approach is necessary to achieve sustainable production, along with improving soil management and increasing economic benefits in the commercial citrus plantations of northern Iran. As the first report, the biological and terrain attributes along with the physicochemical properties (57 soil samples, 0–30 cm) were used for MZ delineation using the integration of principal component analysis (PCA) and the fuzzy c-means clustering methods. An economic analysis based on the MZ results was also performed to determine the changes in each MZ using a relative cost (RC) value. The high correlation between soil properties and terrain attributes and the considerable spatial variation of these factors in the study area call for site-specific nutrient management. The optimal number of MZs was six and there was a significant heterogeneity variation among different MZs. The ranking of the MZs were MZ5 > MZ2 > MZ6 > MZ1 > MZ3 > MZ4 based on higher soil quality and lower costs per tree. The MZ4, MZ3, MZ1, MZ6, and MZ2 required 34.4, 30.6, 29.4, 9.77, and 9.44% more costs than MZ5 (as reference MZ) for achieving similar productivity, respectively. Therefore, this simple and cost-effective approach could be an initial step to utilize fertilizers site-specifically for data-scarce areas and reduce the soil property variability within the delineated MZs, which is fundamental for precision agriculture management.