The data from long-term management and cropping systems experiments are needed to assess changes in soil quality, organic carbon pool, and agronomic sustainability. Thus, a 13-year-old soil fertility management experiment was used to assess the impact of crop residues carbon (C) inputs on SOC stock in a rainfed groundnut (Arachis hypogeae L.)–fingermillet (Eleusine coracana (L.) Gaertn) rotation in semiarid alfisol. The application of farmyard manure (FYM) alone or in a combination with chemical fertilizers contributed to higher amounts of C inputs and subsequently to build up a higher SOC pool. Application of 10 Mg ha−1 of FYM and a recommended dose of chemical fertilizer (25:21.8:20.7 and 50:21.8:20.7 kg N, P, K ha−1 for groundnut and fingermillet, respectively) increased soil SOC pool by 41.2% to 73.0 Mg ha−1 with an increase of 9.3 Mg ha−1 over 13 years. Both SOC pool and rates of its sequestration were positively correlated with cumulative C input and sustainable yield index. A minimal input of 1.62 Mg C ha−1 yr−1 is needed to maintain SOC pool at the antecedent level. Balanced application of NPK fertilizers is needed to reduce and reverse the depletion of SOC pool.