The inoculation of tree species with plant growth-promoting bacteria (PGPB) has emerged as an important strategy for the acclimation of seedlings by improving plant tolerance to biotic and abiotic stresses. This study aimed to evaluate the effects of inoculation with bacterial species (Azospirillum brasilense - Ab-V5, Bacillus sp., Azomonas sp. and Azorhizophillus sp.) on the growth and physiology of the Neotropical tree species Trema micrantha and Cariniana estrellensis under drought conditions. When associated with Ab-V5 and Azomonas sp., T. micrantha showed increased protein in the leaves, starch in the leaves and roots, photosynthesis, instantaneous carboxylation efficiency and root and shoot dry mass. Moreover, there were reductions in hydrogen peroxide, lipid peroxidation, water potential and proline. In C. estrellensis associated with Ab-V5, higher values of photosynthesis and instantaneous carboxylation efficiency were observed, in addition to higher starch content in the leaves and roots and higher protein content in the leaves; lower hydrogen peroxide and lipid peroxidation contents were also observed. The associations of T. micrantha with Ab-V5 and Azomonas sp. and C. estrellensis with Ab-V5 favored the activation of metabolic processes under drought, leading to greater drought tolerance. This work demonstrates the effects of compatible associations of Neotropical tree and PGPB species and suggests that the identification of compatible PGPB strains can result in tree seedlings with increased tolerance to abiotic stresses, such as drought.