Abstract Background Pre-exposure prophylaxis (PrEP) is an effective HIV prevention method and a key component of Philadelphia’s Community Plan to End the HIV Epidemic (EHE). However, significant barriers to accessing PrEP exist among people at risk for HIV. Low-threshold models for PrEP services that minimize barriers to entry and service engagement could help bolster access to PrEP through community-based clinics. This study aimed to describe the initial implementation of low-threshold PrEP services in three sexual health clinics funded by the Philadelphia Department of Public Health and explore strategies for delivering low-threshold PrEP services. Methods We conducted three focus groups with staff (i.e., providers, prevention navigators, and administrative staff, N = 21) at each of three participating PDPH-funded sexual health clinics from November 2021 to January 2022. Discussion topics included details about the PrEP delivery process, clinic strengths and assets, resource gaps, and PrEP implementation goals. Follow-up interviews with staff members (N = 8) between March 2022 and May 2022 focused on identifying successful strategies for PrEP delivery and adaptations needed to optimize low-threshold PrEP service delivery. Rapid qualitative methods and the Consolidated Framework for Implementation Science were used to analyze data from focus groups and interviews. Results Participants collaborated to create process maps that visualized the steps involved in delivering PrEP services within their respective settings. These maps highlighted several stages in PrEP service delivery, such as connecting individuals to services, providing prevention navigation, conducting clinical encounters, and ensuring follow-up care. Participants described effective strategies for implementing PrEP, which included integrating and co-locating services on-site, strengthening staffing resources and capacity, and addressing barriers experienced by clients. Conclusions Lessons from the implementation of low-threshold PrEP service delivery in Philadelphia can guide ongoing local adaptations and future scale-up of these models to improve access to PrEP and advance the goals of the EHE initiative.