Background and aims <p>Rapid SOC enhancement in infertile soils requires substantial organic inputs, which can be efficiently supplied through the granulation of agricultural wastes. However, the mechanisms of granulated organic amendments (GOA) on SOC sequestration and saturation in infertile paddy soils remain unclear. This study aimed to investigate the dynamics of SOC functional pools and saturation under different organic amendment measures.</p> Methods <p>A 2-year field experiment was established including four treatments: control (no amendment), composted manure (10 t ha⁻¹ annually), 20 and 40 t ha⁻¹GOA at the beginning of experiment. The accumulation and stabilization of SOC under different treatments were evaluated via the separated SOC functional pools and the calculated C saturation deficit.</p> Results <p>The application of GOA markedly increased SOC content, particularly by expanding the unprotected C sub-pool (by 20%) in the topsoil (0–20&#xa0;cm). Enhanced microaggregate formation promoted the transformation of chemically and biochemically protected fractions into physico-chemical and physico-biochemical sub-pools, thereby improving C stabilization and sequestration potential. Moreover, granulated amendments enhanced organo-mineral complex formation, increasing stable C saturation and sequestration efficiency. In the subsoil (20–40&#xa0;cm), where lower C saturation permitted higher sequestration efficiency, chemical protection dominated organic C stabilization. After two years, the stable C saturation deficit (Csd) decreased by 40.0% in topsoil and 25.7% in subsoil relative to initial levels.</p> Conclusion <p>A single application of GOA at 40 t ha⁻¹ substantially enhanced SOC saturation and stabilization in infertile paddy soils by modulating functional SOC pools and promoting microaggregate formation, offering an effective strategy for accelerating C accrual in degraded croplands.</p>