IntroductionThe cacao tree (Theobroma cacao), a perennial crop that serves as a source of cacao beans, can suffer from drastic climate changes such as irregular rainfall and shorter rainy seasons. The search for hybrids which are capable of producing specific metabolites favoring adaptation in new climatic conditions is a challenge in cacao farming.ObjectivesWe aimed to (1) analyze the metabolic changes in calli of three cacao genotypes during water deficit induced by incubation with polyethylene glycol and (2) assess their response to water deficit stress with regard to somatic embryo differentiation.MethodsMetabolic profiling was carried out using 1H‐NMR spectroscopy and multivariate data analysis was applied to crude extracts of calli grown in non‐stress or water deficit stress conditions.ResultsWater deficit stress influences the capacity of calli to produce embryos. The SCA12 genotype exhibited the best conversion capacity under severe conditions and was considered as tolerant to drought, followed by the SCA6 genotype (mid‐tolerant) and the MA12 genotype (sensitive). Fifty‐four metabolites were identified in the three cacao genotypes and discriminant metabolites were identified. Metabolites involved in water stress tolerance such as fructose, trans‐aconitic acid, leucine, and hydroxybenzene derivatives were observed in SCA12, the tolerant genotype.ConclusionThese results demonstrate the utility of 1H‐NMR metabolomics as an essential tool for the analysis of the drought tolerance characteristics of T. cacao.