The current study evaluated the differences in soil and biomass carbon (BC) stocks of native forest, annual crop field and coffee based agroforestry at Gera, South-west Ethiopia. A total of 24 sample plots were collected by Stratified random sampling method. After measuring the required parameters; BC (above and below ground), and SOC, texture, bulk density and pH were analyzed. The results showed that, BC significantly varied with land use types. On the other hand, the SOC under native forest and coffee based agroforestry has no significant difference, while it shows significant difference under the annual crop field. The present study indicated that, the total carbon stock in the native forest is greater than coffee based agroforestry which shows much greater difference than annual crop field. This may indicate that, conversion of annual crop field to coffee based agroforestry can increases carbon stock and sequestration potential in the study area.