Cocoa-based agroforestry (AF) systems are a conspicuous element of agricultural landscapes worldwide. Shade canopy analysis and design is a key component of crop husbandry, and requires a good understanding of the interactions, synergies and trade-offs between shade, yield and environmental services. In this chapter we provide a guide and some principles to analyse and design an optimal shade canopy that provides a diverse, resilient AF system. We first review the different cocoa system typologies described in the literature, placing special emphasis on cocoa–timber systems. We present a guide for the analysis of the shade canopy of shaded cocoa systems, and then investigate the optimal design for cocoa shade canopies, with emphasis on the analysis of trade-offs and synergies between carbon storage and cocoa yields. Finally, we consider critical issues in applying AF science/knowledge to cocoa cultivation programmes.