Agroforestry systems (AFS) are recognized as one of the practices with high potential to store carbon in soils. In the Itasy region, AFS were introduced to improve farmers' livelihoods by diversifying income sources and to address problems related to soil degradation. Previous studies in the region have shown the potential of AFS to store organic carbon in the soil. In the present work, we carried out further studies to assess the main factors affecting SOC stocks in AFS. In 2014, we performed a soil sampling on 137 AFS farmers'plots to assess SOC stocks in different AFS. In 2018, a second sampling was carried out to calculate SOC storage rates using the diachronic approach on 30 most representative AFS. The results revealed that the factors "age of the system" and "type of organic inputs" significantly affected SOC stocks in AFS. SOC stocks increased significantly over time in AFS plots, benefiting from regular organic inputs such as manure and/or compost. In contrast, SOC stocks remained unchanged over time in AFS plots where no organic fertilization was used. Our study showed a substantial SOC storage up to 47 parts per thousand year(-1), mainly explained by regular additions of organic inputs to maintain soil fertility and crop production. However, to fully understand the process of SOC storage in this context, further works, such as the analysis of the link between organic matter quality and the SOC storage process, and the quantification of the share of soil carbon inputs derived from tree biomass should be undertaken.