In Côte d'Ivoire, the world's largest cocoa producer, cacao (Theobroma cacao L.) is usually grown from seed. The genetics consist of a mix of amelonado, trinitario and selected hybrids. This mix of varieties generates high phenotypic variabilities, including variability in tree productivity, within cacao populations in both smallholder and industrial plantations. Tree-to-tree variability in yield has been reported in cacao breeding trials under different environmental conditions. However, it has never been considered a limiting factor for agronomical performance of seedling-based cacao plantations. Around 10 000 cacao trees from seven plots under different environmental conditions in a cacao plantation in Côte d'Ivoire were monitored for 2 years. Pod production of individual trees was recorded and annual average tree pod yields were assessed. High heterogeneity in cacao-tree yields was observed in all plots, with coefficients of variation ranging from 56 to 102%. The distribution of cacao-tree yields in each plot was positively skewed. Analysis of these distributions showed that unproductive trees represented a significant proportion of cacao tree populations (7%), and the 20% least productive trees accounted for 3% of production. The 20% most productive trees were responsible for 46% of the total pod production of a plot. This heterogeneity reflects a major imbalance in the agronomical performances of low- and high-yielding trees and also represents possible efficiency gaps in seedling-based cacao plantations, which could be overcome through innovative corrective strategies, opening new pathways for improvement of cacao-based cropping systems.