Regenerative agriculture practices aim to restore soil health through biological processes, yet standardized indicators for assessing soil biological recovery remain poorly defined. This study developed microbial signature profiles as quantitative indicators of soil health across 48 paired sites comparing regenerative and conventional management systems over five years. Regenerative practices included cover cropping, diverse rotations, integrated livestock grazing, and elimination of synthetic inputs. High-throughput sequencing of 16S rRNA and ITS genes identified key microbial taxa that consistently respond to regenerative management. Regenerative systems showed 65% higher microbial diversity (Shannon index: 5.2±0.4 vs 3.2±0.5), enhanced fungal: bacterial ratios (0.8 vs 0.4), and distinct community compositions dominated by beneficial taxa. A microbial health index (MHI) was developed based on 15 indicator species including Rhizobium, Trichoderma, and arbuscular mycorrhizal fungi, achieving 89% accuracy in distinguishing regenerative from conventional systems [4]. Regenerative soils exhibited higher abundances of plant growth-promoting bacteria (+180%), disease-suppressive fungi (+240%), and nitrogen-fixing bacteria (+320%). Functional gene analysis revealed enhanced metabolic diversity with increased genes for nutrient cycling, stress tolerance, and secondary metabolite production. Soil enzyme activities correlated strongly with microbial signatures (R² = 0.82), validating biological functionality. Economic analysis demonstrated that microbial signature-guided management could reduce input costs by $125-280 ha⁻¹ while maintaining yields. Machine learning models using microbial signatures predicted soil carbon gains, aggregate stability, and water infiltration rates with 85-92% accuracy. These findings establish microbial signatures as reliable, quantitative indicators for monitoring soil health recovery in regenerative agriculture systems, providing farmers and researchers with practical tools for assessing biological soil health transitions.