Community engagement involves five phases: informing, consulting, involvement, collaboration, and empowerment. This study explored the experiences of community stakeholders during the collaborative phase of community engagement co-developed by researchers and community members for the implementation of projects. The study was carried out in uMkhanyakude District, South Africa. A qualitative case study approach was used to explore the collaboration phase. Data was collected from key community stakeholders through key informant interviews, focus group discussions, and direct observations. The findings indicated that village headmen, community advisory board members and community research assistants can collaborate as trustworthy partners to address community health challenges. Community research assistants complement the role of participatory-based research appropriately, as they get to be involved hands-on together with the researchers. However, despite the significant role community research assistants played in the projects implemented by the KwaZulu-Natal Ecohealth Program, maintaining collaborative relationships was marred with unforeseen difficulties due to many barriers which included stretched work hours, lack of breaks, miscommunication around compensation, inappropriate behavior from the research team, and humiliation/oppression over language. Initiatives for community-based participatory research have proven to be effective as a collaborative approach that combines methodical research, involvement, and action to address health-related problems. However, it is necessary to consider the local socio-cultural aspects that could lead to barriers and misunderstandings between the locals and the researchers. Collaborative partnerships should ultimately result in community empowerment.