Understanding impact of long-term fertilisation on soil aggregation, carbon (C) stabilisation and temperature sensitivity of soil organic C (SOC) mineralisation are necessary to foresee C dynamics. The present study was conducted in an Inceptisol under wheat (Triticum aestivum) based cropping system, with the objective to quantify the effect of 44 years of integrated nutrient management on soil aggregation, enzymatic activity, and temperature sensitivity (Q10) of SOC. Treatments were: unfertilised control (UC), 100% recommended dose of nitrogen (N), N and phosphorus (NP), N, P and potassium (NPK), integrated application of NPK and farmyard manure (FYM) (NPKF) and 150% recommended dose of N, P and K (1.5NPK). The observed data were analysed using analysis of variance for randomized block design and Tukey’s HSD test (P < 0.05) was used for mean separation. In the 0–15 cm soil layer, plots under NPKF had ˜121 and 19% larger macroaggregate-associated C than UC and NPK plots, respectively. Irrespective of soil depth and temperature, higher cumulative C mineralisation was observed for NPKF (by ˜67-91%) and NPK (by ˜42-56%) treated plots than UC. Activation energies for SOC decomposition in 0–15 cm bulk soil were ˜205, and 258% higher in NPKF, and 1.5NPK, respectively, than UC plots. Mean Q10 of macroaggregate-C was higher than microaggregate-C. Aggregate-C of sub-surface soil was more temperature sensitive than surface soil, possibly due to higher recalcitrant/total SOC in the subsurface than surface layer. Thus, it reveals the need of better C management practices to augment the lability of C in subsurface soil layers. Plots under NPKF had higher β–glucosidase and fluorescein diacetate activities in bulk soils and aggregates over NPK in the both layers. NPKF application is recommended for improved soil aggregation, SOC protection within macroaggregates, enzyme activities in bulk soils and aggregates and capable for less proportional SOC decomposition than NPK or UC plots at higher temperature. Thus, soil management involving organic manure application and mineral fertilisers would enhance the activation energy of SOC and act as a barrier for SOC decomposition by facilitating soil aggregation and enhance SOC sequestration.