Cacao is an understory plant cultivated in full-sun monocultures, multistrata agroforestry systems, where cacao trees are planted together with fruit, timber, firewood, and leguminous trees, or within thinned native forests. In agroforestry systems of cultivation, cacao is subjected to excess shade due to high density, excess growth, and the unmanaged pruning of shade trees. Cacao is tolerant to shade, and the maximum photosynthetic rate occurs at an irradiance of around 400 μmol m−2 s−1. However, excess shade further reduces the irradiance, which is detrimental to photosynthesis and growth functions. Intra-specific variation is known to exist in cacao for the required saturation irradiance. A greenhouse study was implemented with 58 cacao genotypes selected from four geographically diverse groups: (i) wild cacao from river basins of the Peruvian Amazon (PWC); (ii) Peruvian farmers’ collection (PFC); (iii) Brazilian cacao collection (BCC); and (iv) national and international cacao collections (NIC). All of the cacao genotypes were subjected to 50% and 80% shade where photosynthetic photon flux density (PPFD) was 1000 and 400 μmol m−2 ּs−1, respectively. Intra-specific variations were observed for growth, physiological and nutritional traits, and tolerance to shade. Cacao genotypes tolerant to shade were: UNG-77 and UGU-130 from PWC; ICT-2173, ICT-2142, ICT-2172, ICT-1506, ICT-1087, and ICT-2171 from PFC; PH-21, CA-14, PH-990, and PH-144 from BCC; and ICS-1, ICS-39, UF-613, and POUND-12 from NIC. Genotypes that tolerate excess shade may be useful plant types for maintaining productivity and sustainability in agroforestry systems of cacao management.