Conservation of biodiversity and mitigation of global warming are two major environmental challenges today. In this context, the relationship between biodiversity (especially plant diversity) and soil carbon (C) sequestration (as a means of mitigating global warming) has become a subject of considerable scientific interest. This relationship was tested for homegardens (HG), a popular and sustainable agroforestry system in the tropics, in Thrissur district, Kerala, India. The major objectives were to examine how tree density and plant-stand characteristics of homegardens affect soil C sequestration. Soil samples were collected at four depths (0–20, 20–50, 50–80, 80–100 cm) from HG of varying sizes and age classes, and their total C content determined. Tree density and plant-stand characteristics such as species richness (Margalef Index) and diversity (Shannon Index) of the HG were also determined. Results indicated that the soil C stock was directly related to plant diversity of HG. Homegardens with higher, compared to those with lower, number of plant species, as well as higher species richness and tree density had higher soil carbon, especially in the top 50 cm of soil. Overall, within 1 m profile, soil C content ranged from 101.5 to 127.4 Mg ha−1. Smaller-sized HG (<0.4 ha) that had higher tree density and plant-species density had more soil C per unit area (119.3 Mg ha−1) of land than larger-sized ones (>0.4 ha) (108.2 Mg ha−1). Soil C content, especially below 50 cm, was higher in older gardens. The enhanced soil-C storage in species-rich homegardens could have relevance and applications in broader ecological contexts.