Asparagus decline syndrome (ADS) poses a significant threat to asparagus cultivation worldwide. To address this challenge, a two-year investigation was carried out in Spain to assess the impacts of three soil disinfection strategies on asparagus crops. These included biofumigation with seed pellets, biofumigation using poultry manure pellets, and chemical disinfection with dazomet. In addition to evaluating the potential of these treatments to alleviate ADS, the research also focused on identifying the physiological changes linked to the syndrome by examining indicators of oxidative metabolism, hormonal equilibrium, and phenolic compound profiles. Among the treatments evaluated, biofumigation with pellets enhanced vegetative growth, photosynthetic pigment accumulation, antioxidant capacity, and hormonal homeostasis, with these improvements becoming more pronounced in the second year. This approach appeared to promote a healthier physiological status in asparagus plants, likely through improved soil health and reduced biotic and abiotic stress perception. In contrast, chemical disinfection with dazomet, despite initially stimulating some physiological responses, was associated with elevated oxidative stress. Overall, the findings suggest that organic-based soil treatments, particularly biofumigation, represent a promising strategy to strengthen asparagus vigor and resilience against ADS. Further studies are needed to assess their long-term effects in perennial cultivation systems.