Human-induced climate change and erosion of biodiversity are the two most important environmental problems the planet faces currently. The primary driver of global climate change is the rising levels of ambient CO2. India, which ranks third globally in energy consumption and CO2 emissions, has pledged to attain net-zero emission norms by 2070. To become carbon-neutral, the country must reduce its greenhouse gas (GHG) emissions, mostly in the energy segment. However, there are significant GHG releases from the land use, livestock, and food sectors too. Natural climate solutions like agroforestry are becoming increasingly important in the struggle against rising atmospheric CO2 levels. Being multifunctional landscapes, agroforestry has the propensity for climate change adaptation and mitigation, besides conserving biological diversity. Three mechanisms are involved in agroforestry’s capability to mitigate climate change: sequestration, substitution, and conservation of carbon. Tree-based systems hold great promise for carbon sequestration and emission offsetting by replacing fossil energy with biomass. The aboveground C accumulations of Indian agroforestry systems (AFS) varied from 0.23 to 23.55 Mg C ha−1 yr−1, while their belowground stocks ranged from 0.03 to 5.08 Mg C ha−1 yr−1. This implies that, in terms of carbon stocks, AFS are midway between arable agricultural production systems and forestlands. By fostering increased resilience, AFS also can reduce the vulnerability of smallholder production systems. Additionally, AFS can serve as a refuge and stepping stone for the preservation of biodiversity. The high floral diversity (753 taxa across a transect from the coast to the highlands, including 43 species on the IUCN Red List), makes the Kerala homegardens circa situm repositories of species diversity. AFS, therefore, represent a nature-based, “no/low-regrets” option generating medium-to-high profits and medium C stocks for climate change mitigation and adaptation while maintaining farmland biodiversity.