Endophytic bacteria are defined as organisms living at least for a period of their life cycle in the interior of a plant and that can contribute to the health and growth of its host without causing negative effects on their development. It is known that bacterial equilibrium in plant–endophyte interaction could be shifted because some microbial groups are able to use some chemical compounds, such as glyphosate, as a source of energy and nutrients, whereas this herbicide may be toxic to other groups. Therefore, the aim of this work was to assess the diversity of the culturable endophytic bacterial population associated with transgenic glyphosate-tolerant and non-transgenic soybean, with respect to biochemical characteristics and antibiotic resistance. Endophytic bacteria isolated from roots, stems and leaves of non-transgenic and glyphosate-resistant transgenic soybean cultivars were characterized from the biochemical point of view using API kits and the sensitivity to five antibiotics was tested for antibiogram determination. The results from this study showed some differences regarding the β-galactosidase (PNG) use and the assimilation of mannitol (MAN), N-acetyl-glucosamine (NAG), D-maltose (MAL) and potassium gluconate (GNT); a higher frequency of positive assimilation of these compounds was observed in the endophytic bacteria isolated from transgenic soybean. Regarding capric acid (CAP) and adipic acid (ADI) assimilation, positive results were not observed among bacteria isolated from transgenic soybean; a different pattern was observed in bacteria isolated from non-transgenic soybean with a frequency of 35 and 20% bacteria with positive assimilation for PAC and ADI, respectively. Concerning the results about the resistance to antibiotics, both bacteria isolated from non-transgenic and transgenic soybean showed a higher sensitivity to kanamycin, gentamicin and tetracycline, and a resistance range between 50 and 87% to ampicillin. These results suggest that the application at post-emergence glyphosate herbicide on transgenic glyphosate-resistant soybean may interfere with the endophytic bacterial community.