Homelessness is a growing social issue that is a consequence of structural inequities and contributor to the development of health inequities. Community-based research (CBR) has been proposed as an effective research strategy for addressing health equities and promoting social justice through participatory processes. The purpose of this article is to examine the application of CBR principles and practices in the homeless sector and the implications for the production of knowledge and social change to address homelessness. Drawing on our experiences as researchers and service providers, we reflect on the significant successes and challenges associated with using CBR in the homelessness sector. In our discussion we emphasise insights, challenges and lessons learned from a community-university partnership that focused on an evaluation of a transitional shelter program in a large urban centre where housing is expensive and often unavailable.