ABSTRACT Soil organic carbon (SOC) sequestration is vital for food security and climate mitigation. However, its long‐term response to fertilisation remains unclear. Using the 180‐year Broadbalk Experiment (the world's longest‐running fertilisation trial; Rothamsted, UK), combined with 14 C labelling and metagenomics, we identified fundamentally distinct mechanisms of SOC accumulation: a microbially mediated dual pathway under organic fertilisation versus a resource‐limited pathway under inorganic fertilisation. Sustained organic inputs matched inorganic fertilisers in maintaining crop yields while increasing total SOC by 160% (relative to a no‐fertilisation control), far exceeding the 26% gain under inorganic fertilisation. Mechanistically, the continuous supply of labile organic matter provided an energetic surplus, allowing copiotrophic microbial communities with high carbon use efficiency to reduce investment in energy‐intensive enzyme synthesis. This metabolic efficiency facilitated a dual‐pathway expansion, elevating dynamic particulate organic carbon (POC) from 1.4 to 7.5 g kg −1 , while microbial assimilation and necromass accumulation concurrently increased mineral‐associated organic carbon (MAOC) from 6.8 to 21.5 g kg −1 . Conversely, inorganic fertilisation induced an oligotrophic ‘mining’ strategy, in which microorganisms upregulated the degradation of complex organic matter under carbon‐limited conditions, restricting sustained SOC accumulation primarily to the MAOC pool. A global meta‐analysis of field experiments (0–120 years) corroborated these temporal trajectories across diverse soil types, showing that SOC under organic fertilisation increases in a time‐dependent manner, reaching a 77% gain after 80 years (three‐fold greater than under inorganic inputs). Overall, organic fertilisation enhances total SOC via POC and MAOC accumulation, whereas inorganic fertilisation mainly increases MAOC. Long‐term SOC persistence depends not only on carbon inputs, but also on microbial community traits and necromass dynamics, suggesting that aligning nutrient inputs with these biological mechanisms is critical for sustainable carbon sequestration.