Toxoplasma gondii is an intracellular protozoan parasite of veterinary and public health importance. Infection may lead to abortion in susceptible pregnant animals and women, and potentially fatal health complications in immunocompromised individuals. In this study, we aimed to provide an update on the seroprevalence of, and risk factors for, T. gondii antibodies in cattle from Qena, southern Egypt. Additionally, we investigated if raw milk and serum samples from the same animals reacted similarly in a commercial ELISA, thus potentially reducing the invasiveness of future serosurveillance studies. Cattle serum samples (n = 362) from three locations in the Qena governorate (Qena, Qus, and Al Waqf cities), of both sexes and different ages were collected. From most dairy cows, a corresponding milk sample (n = 154) was additionally obtained. We found that the overall seroprevalence in serum samples was 9.1% (33/362). Increasing age was the sole risk factor identified in our study among all tested parameters (location, age, sex, lactating yes or no). Thus, older cattle (more than 3 years old) exhibited significantly higher rates of T. gondii antibodies (11.7%; p = 0.033, odd ratio = 4.3) in comparison to animals younger than 1 year (2.9%). In the corresponding serum and milk samples, the prevalence was 12.3% (19/154) in serum samples, and 9.7% (15/154) in milk samples, respectively. A high correlation was observed between the two sample types with a concordance of 97.4%, a kappa value of 0.87, and a Pearson r correlation coefficient of 0.85. When the serum ELISA was taken as the gold standard, the milk ELISA had the following characteristics: sensitivity (78.9%), specificity (100%), positive predictive value (100%), negative predictive value (97.1%), and area under the receiver operating characteristic (ROC) curve (0.6, p = 0.0011). In this study, we confirmed the frequent occurrence of T. gondii antibodies in cattle in southern Egypt and demonstrated that non-invasive milk samples may be used instead of serum samples for seroprevalence studies in dairy cows.