Purpose Large telehealth companies and smaller aesthetic medicine providers used compounded semaglutide and tirzepatide to meet consumer demand for these drugs during their shortages. In this study, we estimate the documentation rate of compounded formulations of these drugs in the US primary care and characterize differences between users of compounded and brand-name formulations of these drugs. Methods We conducted a retrospective cohort study using data from the American Family Cohort, a nationwide US database of electronic health records from primary care practices, spanning January 1, 2021, to December 31, 2024. Patients with documented semaglutide and/or tirzepatide use were included. Brand-name drug prescriptions were identified from structured data; compounded formulation use was identified from clinical notes. Outcomes included the proportion of patients using compounded formulations and their characteristics. Results Among 153 044 included patients (64.0% female, mean age 55.0 years), 8.2% used compounded formulations, which made up an increasing share of semaglutide and tirzepatide use over time. Users of compounded formulations had longer mean therapy durations (compounded only: 10.0 months vs. brand-name only: 7.8 months) and were more likely to be female, non-Hispanic White, nondiabetic, and to live in areas of lower socioeconomic deprivation compared to patients who used only brand-name drugs. Conclusions Between January 2021 and December 2024, documentation of compounded semaglutide and tirzepatide use in US primary care settings appeared lower than surveys reporting that approximately 23% of patients using these medications received them from compounders. This suggests that many patients may access these medications outside of coordinated care.