Introduction: Although pre-exposure prophylaxis (PrEP) is a remarkable biomedical advance to prevent HIV, ongoing research on PrEP contributes to and interacts with a legacy of HIV experimentation on marginalized communities in resource-limited settings. This paper explores the complexity of PrEP research mistrust among Peruvian transgender (trans) women who completed a PrEP adherence intervention and those who refused participation (i.e. declined to enrol, voluntarily withdrew, and/or were lost to follow-up). Methods: Data were derived from 86 trans women (mean age 29 years) participants in the formative (four focus groups (n = 32), 20 interviews) and the evaluation stages (34 interviews) of a social network-based PrEP intervention for trans women in Lima, Peru. The formative stage took place from May to July 2015, while the evaluative stage took place from April to May 2018. Audio files were transcribed verbatim and analysed via an immersion crystallization approach using Dedoose (v.6.1.18). Results: Three paradoxes of trans women’s participation in PrEP science as a “key” population emerged as amplifying mistrust: (1) increases in PrEP research targeting trans women but limited perceived improvements in HIV outcomes; (2) routine dismissal by research physicians and staff of PrEP-related side effects and the social realities of taking PrEP, resulting in questions about who PrEP research is really for and (3) persistent limitations on PrEP access for trans women despite increasing involvement in clinical trials, fostering feelings of being a “guinea pig” to advance PrEP science. Conclusions: Findings highlight the wisdom inherent in PrEP mistrust as a reflection of trans women’s experiences that underscore the broken bonds of trust between communities, researchers and the research enterprise. PrEP mistrust is amplified through perceived paradoxes that suggest to trans women that they are key experimental participants but not target PrEP users outside of research settings. Findings highlight the urgent need to reframe mistrust not as a characteristic of trans women to be addressed through education and outreach, but as a systemic institutional- and industry-level problem replicated, manifested and ultimately to be corrected, through global HIV science