Soil degradation and nutrient depletion remain pressing threats to sustainable agriculture, particularly in highly weathered volcanic soils where phosphorus (P) retention and structural fragility constrain productivity. This study evaluated the long-term impact of organic amendments (ORG) compared to inorganic fertilization (INORG) across five pasture sites in southern Chile. A comprehensive set of soil health indicators, including physical, chemical, and biological parameters, was assessed alongside plant nutrient status and productivity. Results demonstrated that ORG management significantly improved soil physical structure, reducing bulk density and increasing porosity, water retention, and plant-available water. Chemically, soils under ORG exhibited higher soil organic matter, total carbon, and nitrogen, as well as a 30–40% increase in labile and organic P fractions. Biologically, microbial biomass carbon, nitrogen, and phosphorus increased up to tenfold under ORG, coupled with a 15–50% rise in acid phosphatase activity, indicating enhanced microbial functionality and nutrient cycling. Plant responses mirrored these improvements. ORG-treated pastures produced 25–60% more biomass than INORG-managed sites and showed higher concentrations of N, P, and K in shoots and roots. In addition, elevated chlorophylls and carotenoids supported improved photosynthetic efficiency, while oxidative stress indicators decreased by more than 40%, suggesting greater resilience to environmental stressors. Principal component analysis confirmed that plant vigor, nutrient uptake, and biomass production were strongly associated with organic management, whereas oxidative damage clustered with inorganic fertilization. Overall, these findings provide robust field evidence that organic amendments foster soil resilience and enhance plant performance in temperate pastures. By improving nutrient availability, microbial activity, and water regulation, ORG management emerges as a viable pathway to strengthen agroecosystem sustainability under current and future climate pressures.