Ecohealth projects are designed to garner ownership among all stakeholders, such as researchers, communities, local leadership and policy makers. Ideally, designs should ensure that implementation goes smoothly and that findings from studies benefit the stakeholders, particularly bringing changes to the communities researched. Paradoxically, the process is fraught with challenges associated with implementation. Notwithstanding these challenges, evidence from projects implemented in southern Africa justify the need to invest in the subject of ecohealth. This paper describes and discusses a principal investigator's experience of leading ecohealth projects in Zimbabwe between 2002 and 2005, in Botswana between 2010 and 2014 and in South Africa (ongoing). The discourse is centred on issues of project management and leadership, transdisciplinarity, students' involvement, data management, community engagement, dissemination of research findings and the role of institutions in project management and implementation. The paper concludes that the ecohealth approach is valuable and should be encouraged making the following recommendations; 1) principal investigators must have a good understanding of socio-ecological systems, have excellent project management and writing skills, 2) more than one PI should be involved in the day-to-day running of the project in order to avoid disruption of project activities in the event that the PI leaves the project before it ends, 3) researchers should be trained in ecohealth principles and methodologies at the time of building the research teams, 4) full proposals should be developed with active participation of communities and stakeholders in order to develop a shared vision, 5) involvement of postdoctoral fellows and dedicated researchers with postgraduate students should be encouraged to avoid situations where some objectives are not fully addressed because of the narrow nature of students' work; and 6) citizen science should be encouraged to empower communities and ensure that certain activities continue after project termination.