Toxoplasmosis and chlamydiosis remain among the primary causes of abortion and fetal loss in small ruminants. Consequently, they are a source of considerable economic losses for farmers. The objectives of this study were to determine the seroprevalence and highlight the risk factors associated with
Toxoplasma gondii and
Chlamydophila abortus infection in small ruminants in Cameroon. A cross-sectional study was conducted in 200 small ruminant farms during a period from April to October 2021. A total of 1061 small ruminants were sampled, and the sera obtained were analyzed using the indirect ruminant multi-species ELISA test for specific IgG antibody detection for
T. gondii and
C. abortus at the National Veterinary Laboratory. A questionnaire was constructed to collect information about flock management and risk factors possibly associated with
T. gondii and
C. abortus infection in goats and sheep. Overall, 329 small ruminants tested positive for
T. gondii-specific IgG antibodies and 45 for
C. abortus-specific IgG antibodies with a seroprevalence of 31.1% (95% CI: 28.2–33.8) for
T. gondii and 4.2% (95% CI: 3.0–5.5) for
C. abortus, respectively. However, a significant co-infection of 1.8% (95% CI: 0.37–3.3) was obtained between
T. gondii and
C. abortus (
p = 0.02). Linear regression model analysis revealed that, the seroprevalence of
T. gondii at the flock level was significantly correlated with the region (0.22 CI: 0.17; 0.26) the breeding objectives (0.36 CI: 0.17; 0.56) the level of hygiene (0.11 CI: 0.01; 0.21) and presence abortions (0.55 CI: 0.46; 0.64) on the farms and that of
C. abortus was significantly correlated with the regions (0.01 CI: 0.00–0.02) and degree of abortion on the farms (−0.26 CI: −039; −0.14). At the individual level, a significant correlation was observed between the seroprevalence of
T. gondii and region (−0.09 CI: −0.14; −0.04), species (0.07 CI: 0.01–0.14), sex (−0.11 CI: −0.18; −0.03), age (0.08 CI: 0.04–0.12) and physiological status (0.21 CI: 0.18; 0.24). For
C. abortus seroprevalence, a significant correlation was observed with the regions (0.02 CI: 0.00; 0.03) and breed (0.01 CI: 0.01; 0.02) of small ruminants reared in the northern regions of Cameroon. These results could be used to implement efficient management measures to prevent and control
T. gondii and
C. abortus infection in goats and sheep in Cameroon.
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