This study aimed to evaluate the stability of cacao clone production by analyzing the dynamics of pod production over time. It investigates correlations in multi-year production levels and explores how genetics influence both intra-annual and inter-annual temporal production dynamics of total and healthy pods. To address these questions, data were analysed from a clonal cacao trial conducted over a period of 18 years in Costa Rica. Longitudinal data analysis provided a clearer understanding of the link between yields over successive years. The best-fit model proved to be the ante-dependence model. This model indicated that the correlation between two successive years was relatively stable, and the correlation between years decreased as the interval between years increased. These correlations are also higher as the age of the trees increases. The clones differ more in terms of their production of healthy pods than total pod production. Four dynamic patterns, considering both intra- and inter-annual production, were identified, revealing differences in production timing and distinct peaks for each class. Inter-annual variability analysis revealed differences in healthy pod production among classes, with some displaying more sustainable production dynamics over 18 years. Intra-annual variability analysis showed significant variation in production periods among clones, with different production distributions throughout the year allowing selection of escape and or resistant clones. The study emphasized the importance of genetics in sustainable cacao production, with potential implications for clonal selection. It was suggested to combine clones of different classes to mitigate risks and spread harvests, emphasizing that resilience is a crucial criterion in cacao breeding programs to effectively meet new challenges. Further research is recommended to explore the influence of various environmental factors and facilitate more efficient selection in perennial crops, with the aim of selecting more resilient clones, a particularly important objective in the context of climate change.