This study examined the long-term effects of the Site-Specific Nutrient Management Integrated Plant Nutrient System (SSNM-IPNS) on carbon sequestration, stock, loss and mineralization in soil within a 26-year-old ricerice cropping system at wetland of Tamil Nadu Agricultural University, Coimbatore. The research focused on the impact of integrated organic and inorganic nutrient application on carbon fractions compared to conventional fertilization methods under wetland ecosystems. Results indicated that the SSNM-IPNS approach significantly enhances soil total organic carbon (TOC), with levels reaching 1.56% compared to just 0.78% in control treatments. Furthermore, labile carbon fractions such as permanganate-oxidizable carbon (POx-C), microbial biomass carbon (MBC), water-soluble carbon (WSC), and particulate organic carbon (POC) were found to be greater in the SSNM-IPNS management. Increased rates of carbon mineralization and basal respiration also reflected a more active and efficient microbial community in these soils. Soil microbial indices, including the microbial quotient (qMic) and the metabolic quotient (qCO2), further emphasized the benefits of the SSNM-IPNS approach in enhancing soil health. Overall, the findings demonstrate that SSNM -IPNS significantly improves carbon sequestration, nutrient cycling, and soil fertility, promoting sustainable agricultural practices vital for long-term productivity in intensive cropping systems. This research underscores the importance of adopting innovative nutrient management practices for sustainable agriculture.