Assessing the soil health in agricultural areas is a fundamental task, particularly in the context of climate crisis, where soil degradation is perceived as one of the primary threats facing contemporary society. Proper management of these spaces is a priority action for maintaining food security and achieving sustainable development goals. In this regard, it is imperative to develop sustainable and effective adaptation strategies, understanding the need to promote the application of robust methodologies for monitoring various soil health indicators (physical, chemical, and biological). Thus, it is essential to promote practices and treatments aimed at enhancing soil resilience to new changing conditions. Under this paradigm, this study aims to evaluate the soil health status based on different physicochemical indicators in a representative experimental plot of nectarine cultivation in the province of Zaragoza (Spain). The study investigates the impact of a treatment based on the use of multifunctional cover crops (CCM) on these indicators. Soil samples were collected every two months over three years, evaluating different indicative properties in (i) a control zone (without CCM treatment) and (ii) a zone with CCM treatment (Livingro). The results show the effects of this treatment on the soil. The main analyzed properties indicate that the Livingro-treated zone is improving soil health, particularly in key indicators such as basal respiration, organic carbon, nitrogen, and porosity. Likewise, climatic variability, specifically existing seasonal rainfall differences, has been identified as a determining variable in the results analysis.