Losses of carbon (C) stocks in terrestrial ecosystems and increasing concentrations of greenhouse gases in the atmosphere are challenges that scientists and policy makers have been facing in the recent past. Intensified agricultural practices lead to a reduction in ecosystem carbon stocks, mainly due to removal of aboveground biomass as harvest and loss of carbon as CO2 through burning and/or decomposition. Evidence is emerging that agroforestry systems are promising management practices to increase aboveground and soil C stocks and reduce soil degradation, as well as to mitigate greenhouse gas emissions. In the humid tropics, the potential of agroforestry (tree-based) systems to sequester C in vegetation can be over 70 Mg C ha-1, and up to 25 Mg ha-1 in the top 20 cm of soil. In degraded soils of the sub-humid tropics, improved fallow agroforestry practices have been found to increase top soil C stocks up to 1.6 Mg C ha-1 yr-1 above continuous maize cropping. Soil C accretion is linked to the structural development of the soil, in particular to increasing C in water stable aggregates (WSA). A review of agroforestry practices in the humid tropics showed that these systems were able to mitigate N2O and CO2 emissions from soils and increase the CH4 sink strength compared to cropping systems. The increase in N2O and CO2 emissions after addition of legume residues in improved fallow systems in the sub-humid tropics indicates the importance of using lower quality organic inputs and increasing nutrient use efficiency to derive more direct and indirect benefits from the system. In summary, these examples provide evidence of several pathways by which agroforestry systems can increase C sequestration and reduce greenhouse gas emissions.