Adverse effects caused by drought on cacao seedlings can produce significant yield losses and require a better understanding of plant-tolerance mechanisms in order to overcome them. The selection of drought-tolerant rootstocks is a key strategy to achieve greater resilience in water-limited environments. This study aimed to assess leaf ecophysiological responses and growth of four rootstocks and 24 rookstock-scion combinations to water deficit. Leaf stomatal conductance (gs), leaf water potential (Ψleaf) and relative quantum yield of PSII (ΦPSII) were measured in irrigated and non-irrigated seedlings. Data were recorded 14 and 20 days after irrigation was suspended in the non-irrigated seedlings. Biomass of leaf, stem and root as well root volume were determined 24 days after irrigation was withheld. The EET-400 rootstock showed significantly higher values of Ψleaf at both 14 and 20 days under water deficit. This rootstock and IMC-67 showed the highest gs after 14 days without irrigation The relationship between Ψleaf and gs showed that the combinations of rootstock EET-400 with scions EET-575, EET-576 and EETP-800 exhibited the highest values of gs and Ψleaf. The lower root volumes found under the water deficit condition in EET-400 and IMC-67 demonstrate that tolerance to water deficit by cacao rootstocks is not influenced by a greater contact surface of the root with the soil.