Adenoviruses (AdVs) and the microsporidium Encephalitozoon pogonae have been repeatedly detected in bearded dragons (Pogona spp.). The majority of adenoviruses found in these animals have been characterized as agamid atadenovirus 1 (AgAdV1) in the species Lizard atadenovirus B, although other AdVs have also been described sporadically. Infection with AgAdV1 has been hypothesized to increase susceptibility to other pathogens, and coinfections with microsporidia and AdVs have been described in individual cases. In a retrospective study, samples from bearded dragons submitted to a commercial laboratory (Laboklin GmbH & Co. KG, Bad Kissingen, Germany) for the detection of AdVs by PCR were also screened for the presence of E. pogonae. Samples from 144 animals, mostly cloacal swabs as well as feces and tissue samples, were included in the study. The AdV PCR was positive for 35 (24.3%) samples and the E. pogonae PCR was positive for 28 (19.4%) samples. Sequencing of the products from the AdV PCRs showed that 30 (85.7%) of the viruses detected were identifiable as AgAdV1 and 3 (8.6%) belonged to the species Lizard atadenovirus A; the remaining 2 (5.7%) AdV PCR products were not sequenced. Evaluation of coinfections showed no correlation between infection with an AdV and E. pogonae when all AdV PCR-positive samples were included in the analysis (P = 0.1168), and the correlation remained insignificant when only AgAdV1-like viruses were included (P = 0.0557). AdVs and microsporidia are commonly found in swabs and feces of captive bearded dragons in Europe. Understanding their clinical significance for these animals requires further study.