A study was carried out to assess the efficacy of vaccination, using a phase I Coxiella burnetii-inactivated vaccine (Coxevac®; CEVA), within three goat herds experiencing Q fever abortions waves. The stratification of the population (n = 905) was based on parity and on infection status related to both serological and qPCR vaginal shedding results. Control (n = 443) and vaccinated (n = 462) groups were established in each farm. Vaccination was administered to does before mating and to kids after active immunity acquisition (at least 3–4 months old). The vaccine effectiveness was analyzed at subsequent farrowing on both clinical incidence and vaginal shedding at the delivery day. Among the 231 animals considered as susceptible, that is, seronegative nonshedders, about 90% were infected whatever the group, showing that vaccination did not prevent infection under high infection exposure. Fortunately, vaccination induced an overall decrease in shedding levels. A significant average difference between groups was estimated to 1.16 log(10) bacteria per swab for primiparous and even higher (1.81 log(10)) for initially susceptible ones. Thus, in a clinical context, vaccination should be implemented first in renewal animals. Indeed, young animals are those which best respond to vaccination by significantly reducing C. burnetii burden and, conversely, which excrete bacteria most massively if not vaccinated.