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In Cameroon, cocoa trees are mostly grown in forests and without fertilization. Our aim was to learn more about the temporal dynamics of soils in cocoa agroforests by comparing young (1–4 years old) and old (over 25 years old) cocoa agroforests. Short fallow and secondary forest were used as treeless and forest references. The numbers and diversities of soil vesicular arbuscular mycorrhizal (VAM) fungi on 60 cocoa producing farms in the Central province of Cameroon were assessed based on the classical morphotyping of spore morphology. We also observed the soil organic matter, nitrogen and major soil nutrients. VAM spore density was significantly lower in the young cocoa agroforests (16 spores g−1 dry soil) than in the old cocoa agroforests (36 spores g−1 dry soil). Levels in the nearby secondary forest (46 spores g−1 dry soil) were not significantly different from old cocoa. The spore density was significantly highest in the short fallow (98 spores g−1 dry soil). The Shannon–Weaver index also showed significantly lower biodiversity in young cocoa (0.39) than in old cocoa agroforests (0.48), secondary forest (0.49) and short fallow (0.47). These observations were supported by significant differences in the C:N ratio, Ca, Mg, and cation exchange capacity between young and old cocoa agroforests. We concluded that unfertilized cocoa agroforests could be sustainable, despite a decrease in some soil characteristics at a young stage, due to traditional land-conversion practices based on selective clearing and burning of secondary forest.