This study sought to assess the effects of an inactivated phase I vaccine against Coxiella burnetii at the start of the third trimester of gestation on serological profiles, bacterial shedding patterns and subsequent reproductive performance in dairy cows. Cows were randomly assigned to a control (n = 78) or a vaccinated (n = 78) group on days 171-177 of gestation. Samples of placenta and colostrums at parturition, vaginal fluid, faeces, milk (PCR identification) and blood (anti-C. burnetii antibody detection) were obtained on the day of treatment and on days 91-97 post partum, and also on parturition day and weekly on days 1-7, 8-14, 15-21, 22-28 and 29-35 post partum in a subset of 70 animals. By Kaplan-Meier survival analysis, no significant effect of vaccination was detected on any of the reproductive variables studied. According to the odds ratio, C. burnetii shedding on days 171-177 of gestation was highly correlated with seropositivity against C. burnetii (OR = 9.1), while vaccination was not linked to reduced shedding of the bacterium. In shedders compared to others, the likelihood of pregnancy to first AI decreased and increased by factors of 0.26 and 16.1 on days 1-35 and 91-97 post partum, respectively. In conclusion, when administered at the start of the third trimester of pregnancy, the inactivated C. burnetii phase I vaccine failed to reduce bacterial shedding.