Introduction To advance in their clinical roles, residents must earn supervisors’ trust. Research on supervisor trust in the inpatient setting has identified learner, supervisor, relationship, context, and task factors that influence trust. However, trust in the continuity clinic setting, where resident roles, relationships, and context differ, is not well understood. We aimed to explore how preceptors in the continuity clinic setting develop trust in internal medicine residents and how trust influences supervision. Methods In this qualitative study, we conducted semi-structured interviews with faculty preceptors from two continuity clinic sites in an internal medicine residency program at an urban academic medical center in the United States from August 2018–June 2020. We analyzed transcripts using thematic analysis with sensitizing concepts related to the theoretical framework of the five factors of trust. Results Sixteen preceptors participated. We identified four key drivers of trust and supervision in the continuity clinic setting: 1) longitudinal resident-preceptor-patient relationships, 2) direct observations of continuity clinic skills, 3) resident attitude towards their primary care physician role, and 4) challenging context and task factors influencing supervision. Preceptors shared challenges to determining trust stemming from incomplete knowledge about patients and limited opportunities to directly observe and supervise between-visit care. Discussion The continuity clinic setting offers unique supports and challenges to trust development and trust-supervision alignment. Maximizing resident-preceptor-patient continuity, promoting direct observation, and improving preceptor supervision of residents’ provision of between-visit care may improve resident continuity clinic learning and patient care.