How do long-term fertilization practices alter the channelling of carbon into its fractions across different layers of the soil profile? The potential of soil to sequester carbon is largely determined by how carbon is stored in its fractions. While numerous long-term fertilization studies have investigated carbon fractions, most have primarily focused on the surface soil. Consequently, the extent to which these fertilization practices impact carbon fractions at greater depths within the soil profile remains largely unexamined. This study investigates the impacts of different fertilization practices (100% N, 100% NPK, 150% NPK and 100% NPK+FYM) on different carbon fractions in the deeper layers of soil (0-100cm). The soil samples were collected from an ongoing 51-year long-term experiment that was started in 1971. This study determined total SOC and its fractions including particulate organic matter (POM), light and heavy fraction carbon (LFC and HFC), aggregate associated C, acid hydrolyzable and non-hydrolyzable C (AHC and ANHC), dissolved organic carbon (DOC), fractions of different oxidizability and microbial biomass carbon (MBC). The results showed that 100% NPK+FYM has the highest TSOC stocks up to 100 cm depth. Moreover, 100% NPK+FYM consistently enhanced labile carbon fractions throughout the soil profile (0-100 cm). While all fertilization treatments generally increase carbon fractions, their positive impacts on particulate and density-based organic carbon fractions diminished significantly with increasing soil depth, particularly below 30 cm. Ultimately, our research demonstrates that carbon sequestration and its subsequent persistence in agricultural soils necessitates integrated nutrient management, as evidenced by the sustained positive impact of 100% NPK+FYM on diverse carbon fractions throughout the soil profile, whereas the benefits of chemical fertilizers alone become limited with increasing depth.