Chlamydia abortus (C. abortus) is intracellular, Gram-negative bacterium that cause enzootic abortion in sheep and goats. Information on C. abortus seroprevalence and flock management risk factors associated with C. abortus seropositivity in sheep and goats in Saudi Arabia are scarce. The objectives of this study were to (i) estimate the animal, flock, and within-flock seroprevalence of C. abortus among Eastern Province sheep and goat flocks and (ii) identify the flock management and animal risk factors associated with C. abortus seropositivity in Eastern Province, Saudi Arabia. A cross-sectional study with a two-stage sampling process was carried out in the Eastern Province, Saudi Arabia, between 2015 and 2016. A total of 1717 sheep and 1101 goat serum samples were collected from 21 sheep and 14 goat flocks, then were tested for C. abortus antibodies using a commercial ELISA Kit. In addition, vaginal swabs and aborted tissue samples were collected from sheep (n = 48) and goats (n = 15) with recent history of abortion for detection of C. abortuspmp gene using PCR. A questionnaire was constructed to collect information about flock management and animal risk factors possibly associated with C. abortus infection in sheep and goats. The true sheep and goat-level seroprevalences were 11.1% (95% CI: 9.7–12.7) and 10.6% (95% CI: 8.8–12.5), respectively. The true flock-level seroprevalence was 100% for both sheep and goats. However, the average within sheep and goat flocks true seroprevalences were 9.6% (95% CI: 1.8–22.9) and 9.3% (95% CI: 1.8–19.5), respectively. Multivariable logistic regression revealed that introduction of new sheep to the flocks (OR = 2.6; 95% CI: 1.5–4.4), type of breeding system (OR = 1.8; 95% CI: 1.0–3.4), flocks allowing females in (OR = 1.9; 95% CI: 1.1–3.3) or females out (OR = 2.2; 95% CI: 1.1–4.3), and sheep age 1.4–2.8 years (OR = 1.9; 95% CI: 1.3–2.9) were potential risk factors for C. abortus seropositivity in sheep flocks. However, in goat flocks, the introduction of new goats to the flocks (OR: 1.9; 95% CI: 1.2–3.0) was identified as a risk factor, whereas good farm hygiene (OR: 0.3; 95% CI: 0.2–0.7) was identified as a protective factor. C. abortus pmp gene was identified in 45 (93.8%) and 15 (100%) of samples collected from sheep and goats, respectively. These results could be used to implement efficient management measures to prevent and control C. abortus infection in sheep and goats in Eastern Province, Saudi Arabia, but also could be used to reduce the risk of C. abortus infection in sheep and goat flocks with similar management practices in other regions