Cocoa production in Cameroon has increasingly shifted toward intensified systems reliant on agrochemical inputs, raising concerns about their impacts on soil health and biodiversity. In particular, the use of synthetic fertilizers, fungicides, and herbicides poses significant risks to soil macro-fauna and fertility, both of which are vital for sustaining cocoa productivity. This chapter investigates the effects of agrochemical use on soil macro-fauna diversity and soil fertility indicators in cocoa-based agroforestry systems in the Melong Sub-division, Littoral Region of Cameroon. The study employed a cross-sectional design combining quantitative and qualitative methods. Data were collected through farmer interviews, agrochemical inventories, and soil sampling across three cocoa production systems: conventional monocultures, low-shade agroforests, and diversified agroforests. Soil macro-fauna were identified and analyzed using the Shannon–Wiener Index, while fertility parameters (including pH, organic matter, cation exchange capacity, and available phosphorus) were determined through laboratory analyses. Correlation and regression analyses were used to explore relationships between agrochemical intensity and soil quality indicators. Results showed that diversified agroforests, characterized by minimal agrochemical use, recorded higher macro-fauna diversity and better soil fertility parameters compared to conventional systems. Excessive agrochemical use was associated with soil acidification, reduced organic matter content, aluminum toxicity, and lower macro-fauna abundance. Statistically significant negative correlations were observed between agrochemical application rates and soil pH, macro-fauna diversity, and CEC. The findings underscore the need for ecologically informed cocoa management practices. It is recommended that agrochemical use be minimized and integrated with organic amendments and biodiversity-friendly strategies such as agroforestry. Policy interventions should promote training on sustainable practices, soil monitoring, and farmer incentives for ecosystem conservation. Such measures will support the transition toward resilient, productive, and environmentally sustainable cocoa systems in Cameroon.