A study was undertaken to investigate and mitigate the risk from zoonotic Cryptosporidium associated with dairy farming in Dagoretti division, Nairobi, Kenya. Outcome mapping (OM), a relatively new tool for planning and evaluation, was used to foster and then monitor changes in farmer management of health risks. Elements of the OM framework, including the vision, mission and expected progress markers, were developed in participatory sessions and a set of progress markers was used for monitoring behaviour change in farmers participating in the project (the boundary partners). Behaviour change (the outcome challenge) was supported by a range of awareness and educational campaigns, working with strategic partners (extension agents and administrative leaders). The farmers the project worked with made considerable progress according to the markers; they demonstrated an understanding of cryptosporidiosis, established or maintained clean and well drained cattle sheds, and took conscious effort to reduce possible infection. Farmers who did not participate in the project (non-contact farmers) were found to be less advanced on the progress marker indicators. Non-contact farmers who carried out risk-reducing practices had done so independently of the project team. The administration leaders, as strategic partners, had a positive attitude towards the project and confidence in their ability to support project objectives. The study demonstrates the utility of OM in helping to identify and support behavioural change.