Paratuberculosis, a gastrointestinal disease caused by Mycobacterium avium subsp. paratuberculosis (Map), can lead to severe economic losses in dairy cattle farms. Current measures are aimed at controlling prevalence in infected herds, but are not fully effective. Our objective was to determine the most effective control measures to prevent an increase in adult prevalence in infected herds. We developed a new individual-based model coupling population and infection dynamics. Animals are characterized by their age (6 groups) and health state (6 states). The model accounted for all transmission routes and two control measures used in the field, namely reduced calf exposure to adult faeces and test-and-cull. We defined three herd statuses (low, moderate, and high) based on realistic prevalence ranges observed in French dairy cattle herds. We showed that the most relevant control measures depend on prevalence. Calf management and test-and-cull both were required to maximize the probability of stabilizing herd status. A reduced calf exposure was confirmed to be the most influential measure, followed by test frequency and the proportion of infected animals that were detected and culled. Culling of detected high shedders could be delayed for up to 3 months without impacting prevalence. Management of low prevalence herds is a priority since the probability of status stabilization is high after implementing prioritized measures. On the contrary, an increase in prevalence was particularly difficult to prevent in moderate prevalence herds, and was only feasible in high prevalence herds if the level of control was high.Electronic supplementary materialThe online version of this article (10.1186/s13567-018-0557-3) contains supplementary material, which is available to authorized users.