Deforestation and declining soil fertility are major obstacles for productive cocoa production in West Africa. To improve sustainability of this production system, countries like Ghana promoted agroforestry technologies and introduced organic certification of cocoa agroforests. However, for West Africa, which produces 70% of the world’s cocoa, studies comparing soil fertility under conventional and organic management, which is an important factor for sustainable cocoa production, are rare. Hence this study aimed at investigating differences in soil physico-chemical and microbial properties at 0–10 cm and 10–30 cm depth of traditional cocoa agroforests under organic versus conventional management in four villages with each three farms in Suhum Municipality, Eastern Region of Ghana. Electrical conductivity, soil organic carbon (SOC), total nitrogen (N), SOC/total N, and extractable potassium (K) in the topsoil were 51%, 35%, 30%, 11%, and 47% respectively, lower (p < 0.05) under conventional than under organic management. On average, topsoil under conventional management recorded 29% higher NH4+-N concentration and 27% lower NO3−-N concentrations than topsoil under organic management. Microbial biomass carbon and nitrogen in the topsoil of farms under organic management were 48% and 57%, respectively, greater than under conventional management. Contrarily, conventional management significantly increased the metabolic quotient (qCO2) in topsoil compared with organic management, indicating a higher demand of soil micro-organisms for maintenance energy due to the use of herbicides and pesticides. In cocoa agroforests, conventional management has adverse effects on soil chemical and microbial properties. Hence transitioning from conventional management to organic management is beneficial to maintain soil fertility.