The rapid rise in the number of pet chelonians and their illegal trade can modify the ecology, involving exotic pets, humans, and microbiological agents. Therefore, different epidemiological situations and the related risk to introduce and spread infectious diseases, especially zoonotic agents, have to be considered. The aim of this study was to investigate the microbiological and parasitological situation in 2 chelonian facilities (a private breeding of tortoises and a shelter for turtles) collecting oral/cloacal swabs and cloacal flushes to research viruses, bacteria, and parasites. No Chelonian Herperviruses, Cryptosporidium spp., and Giardia spp. infections were found. Salmonella spp. were detected in 8% of tortoises and in 37.5% of turtles and oxyurid eggs in 23.7% of tortoises and 15% of turtles; ascarid eggs were present only in tortoises. Moreover, 6 turtles showed cutaneous lesions, where Aeromonas sobria was isolated as main pathogen. Further studies should be performed to understand the zoonotic and infectious risk in each chelonian facility and to characterize the variables that could influence the microbiological patterns.