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(1) Background: The objective of this study was to determine the prevalence of <i>T. gondii</i> in meats of cattle, goat and sheep from wet markets in Klang Valley, and abattoirs in Selangor, Malaysia; (2) Methods: A total of 192 meat samples were purchased from 51 wet markets in six districts in Klang Valley (Gombak, Klang, Kuala Lumpur, Hulu Langat, Petaling and Putrajaya). Meanwhile, a total of 200 diaphragm samples were collected from two government abattoirs located in Shah Alam and Banting, Selangor. All meat juices from samples were subjected to an indirect-ELISA kit for the presence of <i>T. gondii</i> IgG antibodies. Furthermore, all 184 meat samples of goat and sheep were subjected to conventional nested PCR (B1 genes) for the detection of <i>T. gondii</i> DNA; (3) Results: <i>T. gondii</i> antibodies were detected in 25% (n = 98/392) of the samples with seroprevalence of 9.1% (19/208, CI: 5.9%–13.8%) in cattle meat; 54.7% (41/75, 95% CI: 43.5%–65.4%) in goat meat and 34.9% (38/109, CI: 26.6%–44.2%) in sheep meat. No <i>T. gondii</i> DNA was detected in any of the meat samples of goat and sheep. <i>T. gondii</i> seropositivity in wet market samples was higher in goat (OR = 37.1 CI 12.4–110.3) and sheep meat (OR 9.03 CI: 3.28–24.8) compared to cattle meat (OR = 1.0) At univariate level, meat from non-licensed abattoirs (OR = 6.0 CI: 2.9–12.3) and female animals (OR = 6.7; CI 1.9–22.6) had higher risks of being seropositive for <i>T. gondii</i> antibodies than licensed abattoirs and male animals, respectively. (4) Conclusions: This is the first report of seroprevalence of <i>T. gondii</i> in ruminant meats for human consumption in Malaysia. The findings signified high exposure of meat samples from wet markets to <i>T. gondii</i> and the need for control measures to reduce the likelihood of infection when such raw or undercooked meats are consumed.