The HIV epidemics in Cambodia is concentrated in key populations (KPs). Pre-exposure prophylaxis (PrEP) has been officially approved in the country since 2019. However, its use may still be controversial after a PrEP clinical trial was interrupted in Cambodia after being deemed unethical in 2004. In this context, it was necessary to evaluate PrEP acceptability and administration preferences of KPs in Cambodia, with a view to increasing roll-out and uptake. We conducted a qualitative study in 2022 comprising six focus groups and four semi-structured individual interviews with transgender women, men who have sex with men, male entertainment workers, venue-based female entertainment workers (FEW), street-based FEW, and PrEP users who participated in a PrEP pilot study that started in 2019. Overall, KPs positively perceived PrEP, with some reservations. They preferred daily, community-based PrEP to event-driven, hospital-based PrEP, and highlighted that injectable PrEP would be a potential option if it became available in Cambodia. We recommend (i) proposing different PrEP regimens and PrEP delivery-models to broaden PrEP acceptability and adherence in Cambodia (ii) increasing the number of community-based organisations and improving the services they offer, (iii) rolling out injectable PrEP when it becomes officially available, and (iv) improving PrEP side effects information.