This cross-sectional study is the first large-scale study on the detection of Q fever to offer an inclusive understanding of the C. burnetii epidemiology among the goats and sheep species in Oman, using serological and molecular techniques. Q fever is a zoonotic and widespread disease caused by Coxiella burnetii, a short gram-negative, coccobacillus that is highly infectious and resistant to harsh environmental conditions. C. burnetii exhibits a variety of antigenic phases, Phase I and Phase II. C. burnetii can infect humans and a wide range of animal species. Nevertheless, goats, sheep, and cattle are the main reservoirs for human outbreaks, and inhalation of contaminated aerosols or dust is the primary source of human infection. The clinical presentation of Q fever differs depending on the species of host. In human and animals, they are mainly asymptomatic except for pregnant ruminants in which reproductive disorders can occur. The aims of the current study were to estimate the seroprevalence of Q fever antibodies and identify the potential risk factors associated with Q fever seropositivity in goats and sheep in the Sultanate of Oman. In addition, evaluate the presence of C. burnetti DNA in blood samples from goats and sheep. The cross sectional study was conducted in the seven governorates of Oman. Enzyme-linked immunosorbent assay (ELISA) was used for screening C. burnetti antibodies in 496 serum samples of goats and sheep and nested-polymerase chain reaction (Nested PCR) was used for detecting C. burnetti DNA in 180 blood samples. Statistical analysis was performed using the chi-squared test, binary logistic regression, McNemar test, and Cohen's kappa test. The overall seroprevalence of Q fever was 45.77%. Q fever seropositivity in goats and sheep was significantly associated with location, age, sex, and recent history of abortion. The highest seroprevalence was in Ash Sharqiyah (66.96%), and the lowest was in Dhofar (2.08%). The finding indicates that Q fever seropositivity was higher in goats and sheep ≥ 2 years than ˂ 2 years. Further, it was found that Q fever seropositivity was higher in female goats (58.5%) and female sheep (42.25%) than in male goats (30.14%) and male sheep (21.15%). Females were 3.1 times more likely to exhibit Q fever illness than males (95% CI: 1.95–5.02; P < 0.05). Out of 496 samples screened for Q fever antibodies, 156 (51.65%) and 71 (36.59%) tested positive for goats and sheep, respectively. The seroprevalence of Q fever in goats and sheep that had a recent history of abortion was 72.13% and 60% respectively. Goats and sheep with a recent history of abortion were 5.1 times more likely to be C. burnetii seropositive compared to healthy animals (95% CI: 3.41–7.48; P < 0.02). The overall molecular prevalence in the study area was 17.78% (95% CI: 12.49%-24.16%). The highest active infection revealed by the PCR was in Ash Sharqiyah (39.70%). There was a poor agreement between ELISA and nested-PCR (kappa value = 0.183). In addition, the McNemar test results shown that ELISA and PCR tests provided significantly different outcomes (p < 0.05). The results of the current study showed that the Q fever in Oman is widely spread. Further studies on C. burnetii infection and genotyping are recommended.