Q fever is a cosmopolitan disease affecting both humans and many animal species. Although sheep are often implicated in human Q fever outbreaks, the disease remains largely underestimated in meat sheep flocks. In order to fulfil this gap, a preliminary study was performed aiming to investigate the serological and molecular aspects of infection with Coxiella burnetii among meat sheep flocks in Belgium. Five Belgian sheep flocks were recruited for this work. Indirect ELISA was used, and in addition, real-time PCR was performed on samples of milk, rectal and vaginal swabs, to understand the dynamics of bacterial shedding. Despite the low overall apparent seroprevalence of 1.39% (95% CI: 0.04–7.5), a high rate of bacterial shedding was found, with 27.7% of tested sheep (N = 72) with a positive result to PCR, especially through the rectal and vaginal routes and in seronegative animals. Furthermore, Coxiella burnetii DNA was detected in 26.76% of seronegative animals. It can be concluded that an overall good clinical condition of the sheep cannot be used to exclude the presence of C. burnetii in a flock. Furthermore in the diagnosis of Q fever in sheep, serology alone was not a sensitive diagnostic tool. On the contrary, molecular biology allowed to detect bacterial shedding, which is an essential element in order to assess the risk due to the contact with shedding animals. At the light of these results, the role of meat sheep flocks in the epidemiology of Q fever in Belgium needs to be better understood.