This study investigates the diversity of soil macro-fauna and its impact on soil fertility within cocoa-based agroforests in Melong sub-division, Littoral region of Cameroon. Utilizing biophysical data collected from farmer-managed plots, we identified a range of macro-fauna including termites, ants, earthworms, woodlice, crickets, beetles, snails, millipedes, spiders, slugs, centipedes, scorpions, and harvestmen. Termites, particularly Coptotermes formosanus and species within the Macrotermitinae, displayed the highest density and diversity, while ants and earthworms showed limited diversity yet high frequency, indicating their ecological significance. Soil fertility assessments, based on physico-chemical analyses, revealed a strong correlation between soil macro-fauna diversity and fertility indices (r = 0.603, p < 0.05). The presence of dominant species such as earthworms, termites, and millipedes significantly enhanced nutrient availability through mechanisms of organic matter decomposition and soil structure improvement. The Stability Index (SI) supported this, revealing a significant relationship with soil fertility (r = 0.617, p < 0.001). The V-index, which measures the impact of tillage on fauna activity, indicated a mild inhibition (V = −0.4), suggesting that the no-tillage practice supports macro-fauna activity and, consequently, soil fertility. This study concludes that maintaining diverse macro-fauna populations is crucial for enhancing soil fertility in cocoa-based agroforests. These findings underscore the importance of integrating biodiversity management in agroforestry systems to promote sustainable agricultural practices and improve soil health.