Yield stability and carbon sequestration of agricultural systems are impacted by nutrient management strategies. Major objectives of this study were to understand the effects of long-term (43 years) manure application on a) environmental parameters such as soil organic carbon (SOC) sequestration, enzyme activities in surface and subsurface layers, and b) yield, and yield stability under a soybean-wheat cropping system in a Vertisol. For this, 100% recommended dose of nitrogen (N), N and phosphorus (NP), N, P and potassium (NPK), NPK + farmyard manure (NPKM) was compared with an unfertilized control (UC) and a fallow land. After 43 years, NPKM and NPK plots had ∼63 and 30% higher total SOC stock than UC, and 45 and 17% higher total SOC stock than fallow plots, respectively in the 0-30 cm layer. Acid hydrolysable C was ~ 42 and 57% higher for NPKM plots in those layers respectively than fallow land. The proportion of macroaggregates was less than 30% in both soil layers of cultivated plots. NPKM had 44 and 28% greater humic and fulvic acidassociated C than fallow land in top layer. Enzyme activities improved in NPKM by ~ 60 and 61% as compared with fallow land. A steady decline in soybean productivity over the years might be due to residue effect. However, wheat yield increased steadily with manuring. Higher SOC accumulation (p < .001), greater enzyme activities (p < .05), improved structure (p < .05) could enhance wheat yield under NPKM. Thus, manure application could lead to yield stability and enhance SOC sequestration in subtropical region simultaneously.