Few studies investigating daily oral preexposure prophylaxis (PrEP) focus on transgender persons. The Sustainable Health Center Implementation PrEP Pilot (SHIPP) Study included a large observational cohort of transgender persons with implications for PrEP in the United States. We examined data from SHIPP’s observational cohort and its Medication Adherence Substudy (MAS) to understand adherence among transgender participants in Chicago, IL. We assessed adherence by the proportion of days covered (PDC) for PrEP medication prescriptions, self-reported interview data, and concentrations of intracellular tenofovir diphosphate (TFV-DP) in dried blood spot (DBS) samples. Between 2014 and 2018, there were 510 transgender participants, 349 (68.4%) transgender women and 152 (29.8%) transgender men. Forty-five of these participants were enrolled in the MAS, 31 (68.9%) transgender women and 9 (20.0%) transgender men. By the 3-month follow up, 100% of MAS participants who completed an interview reported taking 4 or more doses of PrEP in the previous week. At 6, 9, and 12 months, taking 4 or more doses in the past week was reported by 81.0%, 94.1%, and 83.3% of participants, respectively. Results from TFV-DP DBS indicated that fewer participants reached the same level of adherence (4 or more doses/week) at clinical visits compared to self-report and even fewer participants reached this level of adherence based on the calculated PDC. Among participants who remained on PrEP throughout the study, DBS adherence levels declined after the first three months. There remains a critical need to develop strategies to address barriers and interventions that support PrEP adherence among transgender people.