Apparently healthy birds in protected areas in northeastern Brazil were investigated, whether shedding bacterial pathogens to the environment. We determined whether pathogens varied according to the level of the shared habitat human of each protected area, the type of vegetation, hosts’ group and different history traits as migration and foraging behavior, body mass, and sensitivity to human impacts. In addition, we also investigated whether the protected areas were preserving the wildlife from antibiotic-resistant bacteria. For that, oropharyngeal and cloacal swabs were collected from 507 individuals of 91 species. In the culture-dependent method, most of the bacterial isolates belonged to Enterobacterales, with the highest frequency of Klebsiella aerogenes (20.5%) and Escherichia coli (19.3%). There was no relationship between Enterobacterales occurrence according to the type of vegetation, hosts’ group and history traits as foraging behavior (foraging stratum and main trophic category), and body mass, and there was a low association between the protected area and Enterobacterales (φ = 0.17). For Mycoplasma, 10.8% of PCR-tested individuals were positive, with high variation among sampled families, but none of them was positive for M. gallisepticum and M. synoviae. The protected area closer to human settlements presented more resistant isolates to broad-spectrum antibiotics gentamicin (φ = 0.45) and tetracycline (φ = 0.37) and also presented the two positive samples to primary pathogenic Chlamydia psittaci. The birds in the sampled protected areas may host and spread potentially pathogenic microorganisms as C. psittaci and Citrobacter freundii in low frequency in balanced co-existence of host/parasite. However, antibiotic-resistant Enterobacterales in protected areas might represent an impact on its bird populations and on the conservation of the environment.