The role of agroforestry systems in providing ecosystem services is very crucial. The most significant increase in carbon (C) storage is often achieved by moving from lower biomass land-use systems to tree-based systems like agroforestry (AF). However, estimation of carbon stocks in indigenous agroforestry systems of South-eastern Rift- valley landscapes, Ethiopia the data are scarce. The study was aimed to investigate the biomass, biomass carbon (BC), and soil organic carbon (SOC) stock of Enset based, Enset-Coffee based, and Coffee-Fruit tree-Enset based agroforestry systems. Comparison of SOC stock of agroforestry systems against their adjacent monocropping farms was also investigated. The study was conducted in three selected sites of the Dilla Zuria district of Gedeo zone. Twenty farms (total of 60) representative of each AF system were randomly selected, inventoried and biomass C stocks estimated. Ten adjacent mono-cropping farms which were related to each AF system were selected in a purposive manner for comparison of SOC stock. Inventory and soil sampling were employed in the 10×10 m farm plot. The mean aboveground biomass ranged from 81.1 t ha-1 to 255.9 t ha-1 and for belowground biomass from 26.9 t ha-1 to 72.2 t ha-1. The highest C stock was found in Coffee-Fruit tree-Enset based (233.3±81.0 t ha-1), and the lowest was in Coffee-Enset based agroforestry system (190.1±29.8 t ha-1). The result showed that SOC stocks were not statistically significant between the three AF systems, although they showed a significant difference in their BC stock. The AF systems' C stocks are substantially higher than those reported for tropical forests and other AF systems. The SOC of AF systems was significantly higher than the ones for the adjacent monocropped farms. Therefore, it is possible to deduce that AF systems are storing significant amount of C and contributing to climate change mitigation.