The association of different species of endophytic bacteria with the rhizosphere of the host plants can stimulate growth, development and acclimatization, offering a greater quantity of seedlings, in addition to reducing the cycle, providing economic return to the producer. The objective of this study was to evaluate the effect of introduction four bacterial isolates through inoculation into the root system in three banana cultivars (Prata Anã, Grande Naine and BRS Princesa) in the acclimatization phase. The evaluated treatments were: control (nutrient broth without bacteria); Bacillus cereus strain 1 (BC1); Bacillus cereus strain 2 (BC2); Bacillus thuringiensis (BT); Buttiauxella agrestis (BA). The morphological characteristics related to the development of the plants (total height and pseudostem diameter) were evaluated throughout the acclimatization period. After 90 days of transplanting and acclimatization, root length, leaf number, dry root weight, pseudostem and leaf, leaf area, internal carbon concentration, stomatal conductance, photosynthesis rate, transpiration rate, leaf temperature and chlorophyll were evaluated. The bacteria showed different results in relation to the studied cultivars. Considering the morphological and physiological characteristics observed in this study, B. thuringiensis for the cultivars Prata Anã and Grande Naine and the B. agrestis for the cultivar BRS Princesa are recommended for the process of acclimatization of banana seedlings, as they stimulated growth of the plant, increasing the dry mass, besides promoting the growth of roots. In this way, they improved the physiological aspects of the plants and reduced the period of acclimatization of the banana.