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In Mexico, pecan (Caria illinoienensis Wangenh K. Koch) cultivation is considered a primary agricultural activity of great importance, particularly in the state of Chihuahua. Due to the region’s climatic conditions, the soils used for this crop present several limitations that may restrict their agricultural use, as they often exhibit low or null fertility, classifying them as marginal soils. However, these soils can be rehabilitated through appropriate management practices. Among the main recovery strategies are the application of mineral and organic amendments and the use of plant-growth-promoting microorganisms, all of which are considered environmentally friendly alternatives. Therefore, the objective of this study was to identify the types of mineral and organic amendments suitable for the recovery of marginal soils in the agronomic management of pecan cultivation. This study was conducted in the San Cristóbal pecan orchard, located in the municipality of Jiménez, Chihuahua, using a 56 factorial design, reduced to 25 treatments through the Taguchi L25 method. Statistical analysis was performed using response surface methodology, and the evaluated parameters included basic, physical, fertility, and cation-exchange properties of the soil. The results showed that zeolite (19.30 t ha−1) and calcium carbonate (12.70 t ha−1) were amendments that produced the greatest effect on the evaluated parameters. The use of these amendments can significantly complement annual fertilization programs, contributing to meeting the crop’s nutritional demands under a sustainable management approach for pecan production.