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Trees on farmlands and agricultural lands play a crucial role in small holder farmers’ livelihoods in addition to carbon regulation through carbon sequestration. These trees have received much attention recently due to their contribution to climate change mitigation through carbon storage. Quantification of carbon stocks in these trees has always proven difficult due to the spatial extent of these trees and methodological difficulties encountered during measurement. This paper reviews a number of studies done in quantification of biomass and soil carbon stocks in agroforestry within tropics. Most appropriate method employed in determination of carbon stock changes is through use of allometric equations. The equations use parameters like diameter at breast height (DBH), height, crown area which can be measured during field inventory. DBH has always proven to be the best parameter to be used in the equation since it is easy to measure and it does not need expensive equipments. Apart from trees, soils in agricultural lands have the capacity to store carbon and help mitigate effects of climate change. It then identifies the gap that future research can be done for accurate carbon quantification.