Various measures have been advocated for the control of Johne’s disease (caused by <jats:italic>Mycobacterium avium</jats:italic> subsp. <jats:italic>paratuberculosis</jats:italic>, MAP) in different countries. Farmers’ compliance has been reported to be variable depending on disease prevalence and incentives to participate in control programs. After the prevalence of MAP shedding and risk factors for within-herd spread of MAP were assessed in 17 Swiss cattle herds (10 dairy and 7 beef), general and herd-specific recommendations were given to the farmers to reduce MAP transmission within the herd. Participation in the study and implementation of control measures were voluntary, no financial incentives were provided for the realization of control measures. After a 3-year period of monitored observation including biannual farm visits and discussion of the situation, the implementation of the recommended control measures and their effect on prevalence of MAP shedding were evaluated. Implementation of recommended general and farm-specific control measures was only partially realized. Neither the number of animals tested positive (before or during the study) nor the farmers’ knowledge about paratuberculosis were significantly associated with their compliance for the implementation of management changes. The apparent within-herd prevalence remained constant despite limited implementation of control measures, and no particular group of control measures was found to be associated with changes in prevalence. Farmers’ compliance for the implementation of control measures to reduce the impact of Johne’s disease in infected farms was very limited under Swiss farming conditions in the frame of voluntary participation in a research project. These results indicate that the losses associated with paratuberculosis in Swiss dairy and beef operations are not estimated to be high enough by the farmers to justify important efforts for control measures, and that incentives may be necessary to achieve efficient implementation of such measures.