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Soil health underpins food security and climate resilience, yet its management-driven responses remain difficult to quantify at large scales. Here, we present the first georeferenced, national-scale assessment of soil health across Brazil’s croplands, integrating 14,233 data of collected topsoil samples to create a Soil Health Index (SHI). Then, we explored drivers associated with soybean yield performance across the country using SHI data and farmer-reported management practices. Digital soil health mapping at 100 m resolution reveals that cropland soils operate at 71% of their functional potential. Environmental gradients, particularly clay content, altitude, and net primary productivity, define the maximum of attainable soil function. Crop diversification emerged as the strongest driver of synergistic gains: high-performing systems (upper quartile), dominated by rotations combining cash and cover crops, achieved soybean yields nearly twice those of conventional systems. Mechanistic modelling confirmed that crop diversity enhances soil health by increasing soil organic carbon and reducing bulk density, thereby improving soybean yield. This science-based evidence showing that enhancing soil functionality through crop diversification can boost productivity and resilience simultaneously paves the way for encouraging large-scale public and private investments on regenerative agriculture and carbon farming programs in Brazil and other tropical regions worldwide.
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