Q fever is a worldwide zoonosis caused by Coxiella burnetii. Domestic ruminants are considered to be the main reservoir. Sheep, in particular, may frequently cause outbreaks in humans. Because within-flock circulation data are essential to implementing optimal management strategies, we performed a follow-up study of a naturally infected flock of dairy sheep. We aimed to: (1) describe C. burnetii shedding dynamics by sampling vaginal mucus, feces, and milk; (2) assess circulating strain diversity; and (3) quantify barn environmental contamination. For eight months, we sampled vaginal mucus and feces every three weeks from aborting and non-aborting ewes (n=11 and n=26, respectively); for lactating females, milk was obtained as well. We also sampled vaginal mucus from nine ewe lambs. Dust and air samples were collected every three and six weeks, respectively. All samples were screened using real-time PCR, and strongly positive samples were further analyzed using quantitative PCR. Then, vaginal and fecal samples with sufficient bacterial burdens were genotyped by MLVA using 17 markers. C. burnetii burdens were higher in vaginal mucus and feces than in milk and they peaked the first three weeks post abortion or postpartum. Primiparous females and aborting females tended to shed C. burnetii longer and have higher bacterial burdens than non-aborting and multiparous females, respectively. Six genotype clusters were identified; they were independent of abortion status and within-individual genotype diversity was observed. C. burnetii was also detected in air and dust samples. Further studies should determine whether the within-flock circulation dynamics observed here are generalizable.