Bonelli’s eagle (Aquila fasciata) is an endangered raptor species in Europe, and trichomonosis is one of the menaces affecting chicks at nest. In this paper, we attempt to describe the oral microbiome of Bonelli’s eagle nestlings and evaluate the influence of several factors, such as captivity breeding,Trichomonas gallinaeinfection, and the presence of lesions at the oropharynx. The core oral microbiome of Bonelli’s eagle is composed of Firmicutes, Bacteroidota, Fusobacteria and Proteobacteria as the most abundant phyla, andMegamonasandBacteroidesas the most abundant genera. None of the factors analysed showed a significant influence on alfa diversity, but beta diversity was affected for some of them. Captivity breeding exerted a high influence on the composition of the oral microbiome, with significant differences in the four most abundant phyla, with a relative increase of Proteobacteria and a decrease of the other three phyla in comparison with chicks bred at nest. Some genera were more abundant in captivity bred chicks, such asEscherichia-Shigella,Enterococcus,Lactobacillus,Corynebacterium,ClostridiumandStaphylococcus, whileBacteroides,Oceanivirga,Peptostreptococcus,Gemella,Veillonella,Mycoplasma,Suttonella,Alloscardovia,VaribaculumandCampylobacterwere more abundant in nest raised chicks. T. gallinaeinfection slightly influenced the composition of the microbiome, but chicks displaying trichomonosis lesions had a higher relative abundance ofBacteroidesandGemella, being the last one an opportunistic pathogen of abscess complications in humans. Raptor’s microbiomes are scarcely studied. This is the first study on the factors that influence the oral microbiome of Bonelli’s eagle.Supplementary InformationThe online version contains supplementary material available at 10.1007/s00248-022-02002-y.