Soil organic carbon and soil fertility are critical components of soil health and play a significant role in sustaining agricultural productivity. Indigenous agroforestry practices have been identified as an interesting avenue to sequester carbon and enhance soil fertility in tropical smallholder farms. However, that potential remains poorly quantified. To better understand the dynamics of soil organic carbon stocks and fertility, this study evaluated and compared 4 different smallholder indigenous agroforestry systems (i.e., Kihamba, Ginger, Miraba, and Mixed spices) in the northeastern volcanic and block mountains of Tanzania. Specifically, we compared old and young agroforestry systems in terms of soil organic carbon stocks and soil fertility (proxied by effective cation exchange capacity (eCEC)). In each agroforestry system, a network of old and young tree farm plots were selected for soil sampling at different depths and physico-chemical parameters were analyzed (soil organic carbon, texture, bulk density, pH-H₂O, and eCEC). Our findings showed that there was no significant difference between young and old agroforestry systems in terms of soil organic carbon stocks, except in the Kihamba system on the slopes of Kilimanjaro. The highest soil carbon sequestering potential was found in the old Kihamba (located on Nitisols) compared to other systems on Acrisols. Young agroforestry in Ginger and Miraba appeared to have a higher capacity to sequester soil carbon than Mixed spices. Regarding eCEC levels, there was a significant difference between old and young agroforestry systems in both the Kihamba and Miraba system. At the 0–10 cm depth, the highest eCEC levels were found in young agroforestry for Kihamba, Miraba, and Mixed spices. Our results implied that specific management and restoration strategies should focus on optimizing soil fertility and carbon sequestration potential of agroforestry systems in the South Pare and Usambara Mountains characterized by low-fertility Acrisols.