Cacao is an understory plant cultivated under full-sun monocultures to multi-strata agroforestry systems, where cocoa trees are planted together with fruit, timber, firewood, and leguminous trees, or grown within thinned native forests. Under agroforestry systems of cultivation, cacao is subjected to excess shade due to high density of shade trees, and overgrown or unmanaged pruning of shade trees. Cacao is tolerant to shade, and the maximum photosynthetic rate occurs around irradiance of 400 μmol m⁻² s⁻¹ but excess shade reduces the irradiance further 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 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 the 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 might be useful plant types to maintain productivity and sustainability in agroforestry systems of cacao management.