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.