Trees play an important role in influencing soil fertility in agroforestry systems with little research done so far to establish this relationship. This study investigates tree species diversity and soil fertility in cocoa-based agroforests in Cameroon, employing diversity indices, soil fertility analysis as well as correlation and regression analyses. Key findings reveal a total of 50 tree species, with cocoa (Theobroma cacao) as the dominant species, exhibiting a frequency of 1.0 and a density of 0.412 individuals per square meter. The Shannon–Wiener Diversity Index indicated moderate diversity (2.321), highlighting the essential role of species like avocado (Persea americana) and kola (Cola acuminata) in supporting ecosystem health. Strong positive correlations were found between tree species diversity and soil fertility (r = 0.603) highlighting their direct positive relationship. Regression analyses confirmed that increased tree species diversity directly enhances soil fertility (β = 12.517). Policy implications include promoting agroforestry practices that foster diverse species, enhancing both ecological resilience and local livelihoods. There is therefore the necessity of managing agroforests to sustain biodiversity and soil health, ensuring long-term agricultural productivity.