In citizen science, in-depth interviews have advanced the understanding of project leaders’ and citizen scientists’ objectives, motivations, attitudes, and concerns. The issues encountered by researchers conducting in-depth interviews in citizen science are likely not unique to this field. However, these issues can surface and play out in distinct ways that depend on the scientific and sociopolitical circumstances of citizen science communities and projects.Researchers’ experiences conducting in-depth interviews are the subject of a growing literature that describes considerations for conducting research with discrete populations. We aim to contribute to this literature by describing salient practical, ethical, and legal issues to consider when interviewing biomedical citizen scientists, with a focus on bottom-up biomedical citizen scientists who have loose or no affiliations with traditional scientific institutions. These issues concern how to define the interview population; earn trust and demonstrate trustworthiness given past treatment of bottom-up biomedical citizen scientists by traditional researchers and institutions; adapt research practices to the strong culture of openness that characterizes bottom-up biomedical citizen science; and manage potential safety concerns. This essay draws on our own experiences and those of other qualitative researchers and makes suggestions for addressing these issues in ways intended to protect study integrity and demonstrate respect for participants. We also identify questions that would benefit from broad input and continued study. Our objectives in sharing these lessons learned are to support future research and to improve understanding of this exciting participatory space.