Interest in soil health is growing, though the speed and effectiveness of management practices in improving it are uncertain. We measured biological, chemical, and physical indicators of soil health within a working farm zero, five, and nine years after transitioning from regular applications of inorganic fertilizers and pesticides to cover cropping, compost additions, organic amendments, and rotational grazing. We quantified microbial biomass and composition, soil organic matter (SOM), nutrient availabilities, and water stable aggregates in an avocado orchard, a citrus orchard, a pasture, and a vegetable garden. We found substantial and consistent increases in SOM, water stable aggregates, and microbial biomass, especially during the first five years, whereas nutrient availabilities showed no consistent change. Fungal and bacterial communities shifted but not fungal–bacterial biomass ratios or richness. However, fungal guilds responded differently to shifts in management. The biomass of arbuscular mycorrhizal fungi increased in most crops, and fungal saprotroph relative abundance and richness generally increased, whereas putative fungal pathogens showed the opposite response. Overall, we found substantial and rapid increases in indicators associated with improved soil health following the transition from conventional to regenerative management.