Long-term storage of soil organic carbon (SOC) is essential for sustainability of agricultural ecosystems and maintaining overall environment quality as soils contain a significant part of global carbon stocks. In this study, we attempted to explain the carbon mineralization and temperature sensitivity of SOC in maize–wheat systems, a common cropping system in the semi-arid regions of India. Soil samples(0–0.15 m) from long-term experimental plots laid in split plot design with two tillage systems (conventional tillage and bed planting) and six nutrient management treatments (T 1 = control, T 2 = 120 kg urea—N/ha, T 3 = T2 (25 % N substituted by farmyard manure (FYM)), T 4 = T 2 (25 % N substituted by sewage sludge), T 5 = T 2 + crop residue, T 6 = 100 % recommended doses of N through organic source - 50 % FYM + 25 % biofertilizer + 25 % crop residue) were incubated at different temperatures (25, 30, 35, and 40 °C) to determine the thermal sensitivity parameters associated with carbon mineralization. Earlier reports suggest a selective preservation of C3-derived carbon fractions over C4 in the SOC pool, and this is the first instance where δ 13C signatures (C4-derived carbon) were used as a qualitative measure to assess thermal sensitivity of SOC pools in the maize—wheat crop rotation systems of semi-arid India. Among the nutrient management treatments, mineral fertilizers were found to add more C4-derived carbon to the SOC pool in both the tillage systems but shows less promise in SOC stability as indicated by their lower activation energies (Ea) (14.25 kJ mol−1). Conventional tillage was found to mineralize 18.80 % (T 1—control at 25 °C) to 29.93 % carbon (T 3—mineral fertilizer + FYM at 40 °C) during the 150 days of incubation which was significantly higher than bed planting system (14.90 % in T 1—control at 25 °C and 21.99 % in T 6—100% organic sources at 40 °C). Organic manures, especially FYM (19.11 kJ mol−1) and 100 % organics (19.33 kJ mol−1) were more effective in enhancing the Ea of SOC than plots with mineral fertilizers alone (14.25 kJ mol−1), but had relatively higher Q 10 values thereby corroborating the thermal sensitivity hypothesis of recalcitrant organic compounds in soil. Michaelis–Menten derivatives along with thermal sensitivity indicators such as Ea and Q 10 were found to be efficient parameters for explaining carbon mineralization and CO2 efflux from soils.