A judicious management practice to improve the soil's organic carbon level and soil fertility is essential for agricultural and environmental sustainability. The present study was undertaken to assess the long-term effect of various management practices on soil carbon dynamics and agricultural sustainability by computation of indices like carbon pool index (CPI), carbon lability index (CLI), carbon management index (CMI), critical carbon input and carbon budgeting. CMI has been used as a more sensitive indicator to evaluate capacity of a management practice to promote soil quality. Sensitivity index was used to determine the degree of changes in each carbon fraction due to management practices. The study was carried out in a permanent manurial trial plot started in 1964 under a long term rice-rice cropping sequence in Kerala. Based on the results obtained, integrated application of NPK fertilizers along with FYM showed significantly higher carbon indices, increased soil carbon fractions, and carbon sequestration compared to other management practices. The study revealed that applying organics coupled with inorganic fertilizers will manage the SOC level and result in enhanced soil fertility, productivity, and agricultural sustainability.