Community-based participatory research (CBPR) is growing in popularity as a research strategy to engage communities affected by health issues. Although much has been written about the benefits of using CBPR with diverse groups, this research has usually taken place in community-based organizations which offer social services and programs. The purpose of this article is to explore the opportunities and challenges encountered during a CBPR project conducted in a small hospital serving people living with HIV and addictions issues. The structure of hospital-based care delivery required the team to account for participants’ health-related limitations, including adopting recruitment strategies built on clinical care, and modifying the original research design to better protect participant confidentiality in a small space. Although CBPR offers an important strategy for researching with members of hospitalized communities, it requires research teams to develop context-relevant approaches to ethically engaging community members that recognize the ways clinical space mediates the research process.