Despite ongoing investments in the development and testing of new digital interventions for HIV prevention, the widespread use of interventions with proven effectiveness remains limited. This study assessed real-world implementation of a digital HIV prevention intervention, Keep It Up!. The study aimed to identify barriers and facilitators to implementing Keep It Up! within community-based organizations (CBOs) serving racially diverse sexual and gender minoritized populations. The Keep It Up! trial is a type III effectiveness-implementation hybrid trial to compare two delivery approaches: direct-to-consumer and CBO-based implementation. This manuscript focuses on the CBO-based approach through interviews with CBO staff members before and during implementation (n = 37 and n = 25, respectively). Interviews were coded according to the Consolidated Framework for Implementation Research and thematically analyzed. Staff highlighted adaptability, leadership engagement, compatibility, and organizational culture as facilitators of Keep It Up! implementation. Identified barriers included self-efficacy, motivation, staff turnover, and partnerships and connections. CBO infrastructure, capacity, research experience, and processes influenced the relative importance of these barriers and facilitators. This study is one of the first to detail barriers and facilitators experienced by staff implementing a digital HIV prevention intervention in CBOs. Interviews illuminated the need for interventions like Keep It Up! for young men who have sex with men and detailed the need for additional strategies to assist CBOs unfamiliar with implementing digital health interventions. Trial Registration Number: NCT03896776.