Coxiella burnetii and certain members of the Chlamydiales order are zoonotic, intracellular, Gram-negative bacteria, with abortigenic potential in ruminants. These pathogens have a broad host range and worldwide geographical distribution. The current study aimed to reveal the importance of C. burnetii and Chlamydiales spp. in abortions in domestic ruminants and their occurrence in wild ruminants with real-time polymerase chain reaction (qPCR) assays, histology, and immunohistochemical staining (IHC). From the 111 abortion cases of domestic ruminants examined, C. burnetii was detected in 33 placenta samples (cattle, n = 22; sheep, n = 10; goat, n = 1), and members of the Chlamydiales order were detected in 32 placenta samples (cattle, n = 14; sheep, n = 16; goat, n = 2) using qPCR. Coinfection with both C. burnetii and Chlamydiales spp. were identified in 12 cases (cattle, n = 3; sheep, n = 8; goat, n = 1) out of the qPCR-positive samples. The presence of the relevant antigen was confirmed by IHC in 20 cases (C. burnetii, n = 2, in sheep; Chlamydiaceae, n = 17, in sheep [n = 15] and goat [n = 2]; and both pathogens in 1 sheep). Coxiella burnetii was identified in 2.2% (2/91) of the wild ruminants, but the samples were negative by IHC. Uncultured Chlamydiales spp. were detected in 4.4% (4/91) of the placenta samples by qPCR. In conclusion, Q fever is widespread among domestic ruminants in Hungary, and, in several cases, C. burnetii was implicated as the primary cause of abortions. Waddlia chondrophila, Parachlamydia spp., and uncultured Chlamydiales spp. were present only sporadically in samples from cattle and wild ruminants.