Background: HIV pre-exposure prophylaxis (PrEP) has been rapidly implemented in Australia, initially through restricted access in demonstration studies, and then through prescribing across sexual health clinics and general practice settings. In 2018, PrEP was publicly subsidised for people with Medicare (universal health insurance for citizens, permanent residents and those from countries with reciprocal arrangements). There is little research examining the experiences of PrEP providers in Australia, and existing research has been primarily conducted before public subsidy. Methods: In this qualitative study, we examine the challenges that have emerged for PrEP-providing clinicians after public subsidy for PrEP was introduced. We conducted 28 semi-structured interviews in 2019-20 with PrEP providers in two Australian states, and analysed data thematically. Participants included general practitioners (GPs), sexual health nurses and sexual health physicians. Results: Sexual health services have been reconfigured to meet changing patient demand, with an emphasis on ensuring equitable financial access to PrEP. Restrictions to nurse-led PrEP frustrated some participants, given that nurses had demonstrated competence during trials. GPs were believed to be less effective at prescribing PrEP, but GP participants themselves indicated that PrEP was an easy intervention, but difficult to integrate into general practice. Participants expressed discomfort with on-demand PrEP. Conclusions: Our findings indicate that supporting ways for patients without Medicare to access PrEP inexpensively, advocating for nurse-led PrEP, and developing guidelines adapted to general practice consultations could ensure that PrEP is delivered more effectively and equitably. Additionally, PrEP providers require encouragement to build confidence in providing on-demand PrEP.