<p>Agroforestry systems are recognized for their potential to enhance soils organic carbon (SOC) storage and to contribute to climate change mitigation, particularly in tropical regions subject to strong anthropogenic pressure. This study assesses the contribution of agroforestry systems to SOC storage through a comparative analysis between agroforestry systems (croplands with scattered multipurpose trees) and non-agroforestry systems (croplands without tree cover) in Kabare Territory, in eastern Democratic Republic of Congo, an area characterized by high population density and progressive degradation of agricultural soils. A comparative analysis was conducted using 10 plots (five agroforestry plots and five non-agroforestry plots). Soil samples were collected at three depths (0–10, 10–20, and 20–30&#xa0;cm) to determine bulk density, pH, and soil organic carbon, and to estimate carbon stocks. The results show that bulk density increased with depth but remained significantly lower in agroforestry systems across all layers (<i>p</i> &lt; 0.01), indicating improved soil structure. Soil carbon stocks were significantly higher under agroforestry systems, reaching approximately 35.4 ± 4.2 t C ha⁻¹ compared to 25.1 ± 3.8 t C ha⁻¹ in non-agroforestry systems at 0–10&#xa0;cm, with similar trends at greater depths. A strong positive relationship was observed between SOC content and carbon stocks (R² &gt; 0.90), while bulk density showed a negative relationship with carbon storage. Soil pH had no significant effect on carbon stocks. These findings demonstrate that agroforestry systems significantly enhance soil carbon storage and improve soil physical properties. In the context of the Congo Basin, agroforestry represents a viable strategy for soil restoration, sustainable agricultural intensification, and climate change mitigation.</p>