ABSTRACT Soil Organic Carbon (SOC) is an important indicator for soil health and quality. The present study was conducted in five-decade-old Long-Term Fertilizer Experiment involving the finger millet−maize cropping sequence in an Inceptisol to examine the effects of inorganic fertilizers and manures on soil organic carbon stock in relation to C sequestration. This study was based on 10 treatments: 50%NPK, 100%NPK, 150%NPK, 100%NPK + HW, 100%NPK + ZnSO4, 100%NP, 100%N, 100%NPK + FYM, 100%NPK (− S), and control. We assess the clay mineral interaction with soil organic carbon stock and soil enzyme activity. The semi-quantification and characterization of clay minerals were sourced from X-ray diffraction (XRD) analysis, and the SOC stock was calculated based on SOC concentration, Bulk density, and Depth. From the study, results revealed that clay minerals were studied by XRD and FTIR spectroscopy analysis. The results revealed that dominant clay minerals in the experimental soil were in the order of Montmorillonite, 2:1 interstratified minerals, Vermiculite, and Illite, and the buildup of SOC stock raised from 6.3 Mg C ha−1 to 12.9 Mg C ha−1 over five decades. The maximum SOC stock of 12.9 Mg ha−1 was recorded in 100% NPK + FYM while the control registered 7.5 Mg C ha−1. The study conclude that balanced fertilization of 100% NPK with FYM contributed toward the increase in SOC, SOC stock, and carbon sequestration for improving soil fertility status.