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Regenerative agriculture is widely recognized as a promising strategy for restoring soil structure and enhancing soil organic matter (SOM) stabilization; however, its integrated effects along the soil profile and across contrasting soil textures remain insufficiently understood. This study applied a multivariate approach to evaluate soil aggregation and SOM dynamics under regenerative agricultural systems, compared with native forest reference areas, in clayey and sandy soils, with sampling down to 100 cm depth. Soybean–cotton systems under no-tillage with 1, 6, and 10 years of adoption were evaluated in clayey soils, along with soybean–pasture rotation (3-year) and soybean–cotton (1-year) systems in sandy soils. Soil aggregation indicators and SOM pools were integrated through principal component analysis, incorporating SOM functional groups derived from Fourier-transform infrared spectroscopy (FTIR). The PCA revealed a consistent vertical pattern of soil recovery. In surface layers (0–20 cm), regenerative systems were associated with higher macroaggregation, structural stability, and particulate organic carbon, strongly linked to polysaccharide-related bands (~1030 cm⁻¹) and aliphatic compounds. At greater depths (30–100 cm), mineral-associated organic carbon and the fine fraction predominated, aligning with aromatic and carboxylic functional groups, particularly in clayey soils. Overall, regenerative agriculture promoted a vertically structured recovery of soil aggregation and SOM dynamics, with important implications for soil carbon Monitoring, Reporting, and Verification (MRV) frameworks.
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