Our study evaluated the effects of Acacia auriculiformis agroforestry fallows installed on impoverished sandy soils of the Bateke Plateau in the Democratic Republic of the Congo (DRC). We compared physico-chemical properties and carbon stocks of soils under 1 to 3, 3 to 5 and 5 to 7 yr-old Acacia auriculiformis fallows and 5 yr-old savanna fallows. Soils were collected at depths of 0–10 cm, 10–40 cm and 40–100 cm and analyzed for the following parameters: soil organic carbon (SOC), nitrogen (N), available phosphorus (P), exchangeable cations (Ca2+, Na+, K+, Mg2+), cation exchange capacity (CEC), pH (H2O and CaCl2), granulometry and bulk density. In general, results obtained showed that agroforestry fallows are superior to traditional fallows for most measured parameters. The presence of A. auriculiformis improves the chemical properties of the soils compared to savanna soils; soil C and N concentrations as well as cation exchange capacity (CEC) were higher (P < 0.0001) under agroforestry soils than under savanna soils, especially between 0 and 10 cm depth. Our results also showed that A. auriculiformis agroforestry fallows stored 1.5 times more soil carbon than savanna fallows between 0 and 100 cm depth with 75, 106, 114, and 106 Mg C ha−1 respectively for savanna, 1–3 years, 3–5 years, and 5–7 years fallow soils. However, establishment of A. auriculiformis agroforestry fallows resulted in a decrease in soil pH compared to savanna soils. Differences in age and depth of the agroforestry fallow soils did not influence the physico-chemical properties evaluated. Overall, our results show that the establishment of A. auriculiformis agroforestry fallow improves the physico-chemical properties and increases soil carbon stocks compared to traditional savanna fallow. Therefore, we suggest the scaling up of the A. auriculiformis agroforestry improved fallow as a soil regenerative agrotechnology in the tropics.