Prolonged droughts threaten ecosystem functioning by altering productivity, nutrient cycling, and plant-soilmicrobial interactions. However, ecosystem components may respond at different scales, generating decoupled above and belowground responses. In semi-arid regions, shrubs form fertility islands that modulate soil properties and microbial communities, potentially buffering stress. We examined 13-year megadrought effects on shrubland structure, soil microbiota, and nutrients in a Mediterranean-type ecosystem using a before-after (2009-2023) multiproxy design including remote sensing, field assessments, and DNA metabarcoding. We evaluated how the nitrogen-fixing shrub Retanilla trinervia influences soil dynamics relative to bare soils. While overall shrub cover did not decline significantly, vegetation greenness decreased. Despite drought, soil nutrient pools showed no generalized depletion; instead, soil organic carbon and nitrogen increased beneath shrubs, where temperatures were significantly lower. Microbial composition differed between microsites, with shrub soils supporting higher abundances of plant-growth-promoting taxa like Rhizobiales and Penicillium. These findings indicate that while greenness was negatively affected, soils exhibit transient resilience. R. trinervia functioned as a persistent fertility island, modulating microclimate and increasing nutrient pools despite prolonged aridity. Our study highlights how shrub-mediated microsites maintain soil stocks and microbial diversity, suggesting these patches enhance ecosystem resistance to future drought in water-limited environments worldwide.