This study aimed to investigate the presence of beneficial microorganisms in the micropropagation of Pyrus communis rootstocks through the isolation, identification, and selection of auxin-producing bacteria. The selected microorganisms were also inoculated in vitro to evaluate their effect on the plant rooting process and their behavior during the acclimatization phase. The results showed the presence of endophytic microorganisms in plant tissue cultures of the ‘OH×F87′ and ‘PDW’ selections. A low diversity was observed in the population of microorganisms isolated from the in vitro culture of the ‘OH×F87’and ‘PDW’ selections, with a predominance of the genera Acinetobacter, Bacillus, and Buttiauxella. The selection of promoting microorganisms was performed based on the auxin production test, in which 30.36% of the microorganisms tested positive. In the in vitro inoculation, it was possible to observe the promotion of growth and emission of roots in the pear rootstocks, from the inoculation with bacteria identified as capable of producing auxin. This process can be used to replace the inclusion of synthetic auxin in the productive chain of woody fruit trees propagated by vegetative means, such as pears. None of the bacterial isolates was notably more promising, but the general similarity of treatments containing the A. septicus and A. ursingii strains, with the synthetic auxin treatment, suggests the possibility of its use on a large scale allowing the adoption of the cheaper method. of rooting. This work opens the door for further research using new, more promising microbial isolates, and also for lower-cost microorganism cultivation techniques, such as low-cost media obtained from agro-industrial residues.