Soil organic matter links diversification to crop yield through soil health functions in tropical agroecosystems

Soil organic matter (SOM) is a central regulator of soil multifunctionality and agroecosystem resilience under increasing climate variability, yet the mechanisms linking diversification, SOM, and crop productivity remain poorly resolved. Here, we disentangle the soil-mediated pathways through which agroecosystem diversification influences crop yield and yield stability, explicitly positioning SOM as a key mediator within soil functional networks. Thirteen farmer-led experiments under contrasting diversification intensities were evaluated in a tropical region highly exposed to climatic extremes. Topsoil samples (0–10 cm) were analyzed for twelve chemical, physical, and biological indicators. Exploratory Factor Analysis integrated these indicators into four latent soil function constructs representing SOM-driven multifunctionality. Structural Equation Modeling quantified the direct and indirect effects of diversification on crop yield and crop instability via SOM and soil functions. Latent soil functions explained 79% of the variance in soil health, while crop yield was explained at 66% by the full model. Diversification increased SOM, which enhanced soil functions and reduced crop instability. SOM linked diversification to dominant physical, biochemical, and hydrological regulatory pathways, including pore connectivity, microbial functioning, and soil water storage. Reduced crop instability exerted a strong positive effect on yield, highlighting the role of SOM-centered soil resilience. Diversified systems achieved yields up to 2.5 times higher than the state average, indicating that SOM-mediated soil functioning is central to sustaining productive and stable tropical agroecosystems under climate stress.