The control of Q fever, a zoonotic disease caused by the Coxiella burnetii bacterium, remains a scientific challenge. Domestic ruminants are considered the main reservoir, shedding C. burnetii essentially through parturition products during abortion or birth. Sheep are particularly frequently associated with human outbreaks, but there are insufficient field data to fully understand disease dynamics and instigate efficient control measures. A longitudinal follow-up study of a naturally infected sheep flock was performed in order to: (a) investigate relationships between seropositivity and bacterial shedding in the vaginal mucus, (b) describe the kinetics of antibodies, including responses to vaccination, (c) monitor maternal antibodies in ewe lambs, and (d) compare serological results in milk and serum samples. For eight months, we collected blood samples every three weeks from 11 aborting and 26 non-aborting dairy ewes, 20 non-aborting suckler ewes and nine ewe lambs. Individual milk samples were also obtained from lactating females. All serum and milk samples were tested by ELISA whereas vaginal swabs were tested by quantitative PCR. We found that some dairy females did not seroconvert although they shed C. burnetii in their vaginal mucus or despite vaccination. Overall, antibody levels in adult females were found to remain stable over time, with exceptions during the mating and lambing periods. Maternal antibodies decreased during the first month after birth. Interestingly, antibody levels in milk were correlated with those in serum. This study provides valuable field data that will help improve Q fever surveillance and within-flock management measures. Importance Field data are necessary to improve the surveillance, diagnosis and sanitary management of Q fever in livestock. Here, we provide extensive serological data obtained from serum and milk samples of infected and vaccinated ewes belonging to a naturally infected flock of sheep. We show that antibody levels are stable over time and that seropositivity and vaginal shedding are not clearly correlated, whereas antibody levels in milk are strongly correlated with those in serum. Accordingly, we find that antibody levels in bulk tank milk are consistent with the variations observed in the serum of dairy females over time. For the first time, we report the existence of maternal antibody transmission to ewe lambs and we show that the presence of maternal antibodies at birth does not impact the serological response to vaccination at the age of 4 months. Finally, we report that adult ewes generally seroconvert after vaccination, including during pregnancy.