Long‐Term Organic Matter Additions Increase Soil Health and Rice Yield in a Tropical Paddy Soil by Enhancing Carbon Transformation Functions

Although the importance of organic matter management for sustainable rice production is well established in upland soils, its role in lowland paddy systems with gleyed soils remains less understood. To address this gap, we used a 24‐year field experiment in northern Vietnam to examine how organic matter inputs in rice–soybean rotations influenced soil health indicators and crop yield. Topsoil was collected from six treatments: no fertiliser, mineral fertiliser and mineral fertiliser plus cow manure, each with or without crop residue retention. Carbon transformation, nutrient cycling and soil structure maintenance were evaluated using Biofunctool, which integrates eight indicators into a soil health index. Soil macrofauna communities were also assessed. Labile organic carbon was the most sensitive indicator of carbon transformation, increasing more than threefold with organic matter additions compared to the unfertilised control. Organic matter additions also significantly improved macroporosity and water infiltration. The highest nitrate availability occurred under mineral fertilisation combined with residue retention. Overall, organic matter inputs increased the soil health index by 22%, exceeding the effect of mineral fertilisation alone, while residue retention increased the index by 8%. Rice yield increased from 1.8 to 3.4 t ha −1 corresponding to gains of 67% under mineral fertilisation, 90% with manure addition and 10% with residue retention. In contrast, soil macrofauna communities were unaffected by management practices and showed few relationships with soil functions. Rice yield was positively related to the soil health index ( ρ = 0.80), carbon transformation ( ρ = 0.75) and structure maintenance ( ρ = 0.68), whereas its relationship with nutrient cycling was not significant. Together, these results highlight the importance of long‐term organic matter inputs for soil health and rice productivity in gleyed paddy soils, with yield being most strongly associated with carbon transformation.