We aim to determine the effect of long term application of organic and inorganic nutrients on carbon sequestration and related biological attributes of a semi-arid tropical soil under an intensive maize-sunflower cropping system in India. The century-old experimental soil was assessed the impact of nutrient management on carbon sequestration, labile and passive pools of soil organic carbon, and soil biological attributes. The topsoil (0–25 cm) and subsoil (25–50 cm) samples from unfertilized (control), chemical fertilizer applied (IC), organic manure amended (OM), and integrated nutrient management adopted (INM) plots were analyzed for carbon sequestration and dynamics. The INM and OM treatments had a mean annual carbon sequestration rate of 0.18 Mg and 0.14 Mg carbon per ha, respectively. The continuous addition of organic amendment (12.5 t ha−1 year−1 of farmyard manure) with or without chemical fertilizer improved both topsoil and subsoil active carbon pools viz., microbial biomass carbon, labile carbon, water-soluble carbon, particulate carbon fraction, and passive pools like humic acid and fulvic acid significantly compared to synthetic fertilizer and unfertilized treatments. The Fourier-transformed infrared spectra of humic acids extracted from OM and INM treatment soils showed high humification, aromaticity, and redox with complex functional groups than IC and control treatment soils. OM and INM treatments significantly enhanced the abundance of carbon mineralizing gene (chiA) in topsoil and subsoil than IC and control treatments, while the carbon dioxide fixing gene (cbbL) had no apparent change due to nutrient management. Subsequently, the organics amended soils had better biological quality in terms of higher soil enzymes' activity, bacterial abundance, and respiration rate with lower metabolic quotient than chemical fertilized and control soils. The principal component analysis indicated that OM and INM treatment soils were distinctly positioned from IC and control treatment soils and the soil carbon fractions and soil enzymes were the significant factors influencing the nutrient management induced carbon sequestration. The active and passive carbon fractions, dehydrogenase, fluorescein diacetate hydrolysis, alkaline phosphatase, and substrate-induced respiration showed a strong and positive correlation with carbon sequestration of semi-arid tropical soil. Altogether, these findings indicated that the continuous addition of organic amendments would be a valuable practice to improve the soil carbon sequestration and carbon pools, and this practice is essential for the tropical soils with intensive farming to sustain the soil quality and agricultural productivity.