The application of organic amendments in agroecosystems has been widely recommended, but the impact of their C/N ratio on the stabilization and sequestration of soil organic carbon (SOC) is often unaccounted for. The influence of the C/N ratio of amendments on soil physicochemical properties in a rice ( Oryza sativa var. NDR97)-barley ( Hordeum vulgare var. Lakhan) rotation tropical dryland agroecosystem was compared with an undisturbed grassland. Chemical fertilizer in the form of urea and three organic inputs ( Sesbania aculeata shoot, low C/N ratio; air-dried straw of wheat ( Triticum aestivum var. Malviya 533), high C/N ratio; and S. aculeata shoot+wheat straw, high and low C/N ratio combined) carrying an equivalent amount of N, were added to plots of the agroecosystem once during each annual cycle. Soil water-holding capacity (WHC), porosity, SOC, total N, and aggregate stability were improved in the wheat straw and S. aculeata shoot+wheat straw treatments, reaching levels comparable with the grassland. Soil WHC, porosity, and SOC influenced the productivity of the grassland and the agroecosystem. The grassland recorded highest SOC (53% higher relative to control) followed by the wheat straw (+47%), S. aculeata shoot+wheat straw (+37%) and soil total N was greatest in the S. aculeata shoot+wheat straw treatment (+37.5%). Aggregate stability and macroaggregate distribution were also higher in the wheat straw and S. aculeata shoot+wheat straw treatments, however, the microaggregate and silt+clay fractions showed a reverse trend. Management practices with a higher residue-C return in the agroecosystem resulted in increased aggregate stability and aggregate-associated SOC, with C storage attaining levels similar to the natural system.