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Cacao cultivation in the Brazilian Amazon is constrained by nutritional imbalances and a high incidence of witches’ broom disease. Understanding how nutrient status influences disease tolerance and yield is essential for improving productivity. This study aimed to evaluate the relationship between nutritional balance, productivity, and witches’ broom incidence among 25 cacao (Theobroma cacao L.) clones cultivated under Amazonian conditions, using a randomized block design with three replicates (25 clones × 3 blocks), established in a Acrisol, to identify genotypes combining high yield and nutritional homeostasis. Productivity traits, pod disease incidence, and foliar concentrations of macro- and micronutrients were assessed during the fruiting stage. Nutritional status was evaluated using the Compositional Nutrient Diagnosis (CND) method, and multivariate analyses were applied to explore relationships among variables. Significant variation was observed among clones in productivity and disease incidence. Clone EEOP 96 exhibited the highest incidence of witches’ broom and a reduction in yield relative to the most productive clones, reflecting greater disease-related losses rather than generalized nutritional imbalance. In contrast, clones EEOP 63 and EEOP 65 showed superior productivity and lower disease incidence, associated with a more balanced nutritional status and lower nutritional imbalance index. Principal component and clustering analyses confirmed strong associations among nutrient balance, disease tolerance, and yield performance. Cacao genotypes modulate their tolerance to witches’ broom through differences in nutritional homeostasis and productivity. Selecting nutrient-efficient clones such as EEOP 63 and EEOP 65 can enhance both disease tolerance and sustainable cocoa production in the Amazon by integrating clonal selection with nutritional management strategies adapted to regional edaphoclimatic conditions.