This study aims to assess the physico-chemical properties of soils in cocoa-based agroforestry systems in Cameroon, with a focus on two representative profiles, Lelem-Moatong (P1) and Mouanguel (P2), located in the Melong sub-division of the Littoral region of Cameroon. The goal is to understand the impact of different parent materials and agroforestry practices on soil health and fertility in cocoa-based agroforests. A multi-stage sampling approach was employed, with data collection methods combining household surveys, field measurements, and soil sample collection from 14 cocoa-based agroforests. Soil properties, including texture, organic matter, pH, nitrogen content, and cation exchange capacity, were analyzed through standard physico-chemical techniques. Findings revealed that soil texture ranged from clay to loam, with high porosity (60.4–79.9%) promoting good aeration and water retention. Organic matter content averaged 4.93%, while total nitrogen was low (0.1%). Both soil profiles were acidic (pH 4.0–6.0), limiting phosphorus availability due to high solubility of aluminum and iron. The soils exhibited high cation exchange capacities (11.88–38.92 cmol(+)/kg), indicating good nutrient retention. The study underscores the importance of tailored fertilization strategies, particularly for phosphorus, to address the challenges posed by soil acidity. Promoting organic amendments and enhancing soil structure through agroforestry practices can improve soil health and sustainability in cocoa production. Future research should focus on long-term soil monitoring to better understand the impact of agroforestry practices on soil fertility.