Soil organic matter dynamics in terrestrial ecosystems are controlled by complex interactions between various factors such as climate, soil, and agricultural management practices. We utilized a process-based crop model, APSIM, to simulate long-term soil organic carbon (SOC) dynamics for a soybean-wheat cropping system under nitrogen (N) and farmyard manure management (FYM) practices for a 43-year old experimental dataset in India. The APSIM was parameterized and validated to predict grain yield and SOC stock. The validated model was then used to evaluate the impacts of different management practices on SOC dynamics in the top 30 cm of soil through scenario modeling. The results of the APSIM simulations demonstrated that improved N and FYM management practices had great potential to increase SOC sequestration in these Vertisols. The equilibrium SOC concentration under different N management practices increased with a higher N application rate, with the integrated application of N with FYM showing the maximum rate. The optimum N (Nopt) rate for maximum SOC sequestration was estimated to be 155 kg ha−1 for wheat in the studied Vertisol and the time to reach steady-state of the site was 104 years. The Nopt increased SOC by about 28.6% over the initial concentration. We found that the APSIM was robust in predicting long-term changes in SOC stock (Index of agreement = 0.79 and root mean square error = 3.33 Mg ha−1, R2 = 0.92, mean bias error = −1.08) for a Vertisol soil of central India, in this case under a soybean-wheat cropping system. The study results highlighted that balanced fertilization is the key to sustaining SOC stock in the long-term for Vertisols. •Fortythree years of measured SOC stock was satisfactorily simulated by the APSIM model.•Time to reach steady state of SOC stock varied from 37 to 104 years under different N management.•Maximum SOC saturation value of 48.65 Mg ha−1 was obtained in integrated nutrient management involving farmyard manure.•Optimum N application rate for maximum soil C sequestration was 155 kg N ha−1 for wheat and 20 kg N ha−1 for soybean.