Research Highlights: Agroforestry systems in the humid tropics have the potential for high rates of production and large accumulations of carbon in plant biomass and soils and, thus, may play an important role in the global C cycle. Multiple factors can influence C sequestration, making it difficult to discern the effect of a single factor. We used a modeling approach to evaluate the relative effects of individual factors on C stocks in three agricultural systems in Kerala, India. Background and Objectives: Factors such as plant growth form, management, climate warming, and soil texture can drive differences in C storage among cropping systems, but the relationships among these factors and their effects are complex. Our objective was to use CENTURY, a process-based model of plant–soil nutrient cycling, in an experimental mode to evaluate the effects of individual factors on C stocks in soil and biomass in monocultures (annuals or trees) and agroforestry systems. Materials and Methods: We parameterized the model for this region, then conducted simulations to investigate the effects on C stocks of four experimental scenarios: (1) change in growth form; (2) change in tree species; (3) increase in temperature above 20-year means; and (4) differences in soil texture. We compared the models with measured changes in soil C after eight years. Results: Simulated soil C stocks were influenced by all factors: growth form; lignin in tree tissues; increasing temperature; and soil texture. However, increasing temperature and soil sand content had relatively small effects on biomass C. Conclusions: Inclusion of trees with traits that promoted C sequestration such as lignin content, along with the use of best management practices, resulted in the greatest C storage among the simulated agricultural systems. Greater use and better management of trees with high C-storage potential can thus provide a low-cost means for mitigation of climate warming.