With the extensive public, commercial and scientific interest from what has been widely termed the psychedelic renaissance, it is important that the scientific practices and results obtained from its implementation into medicine are put under a critical microscope. While there are numerous works on the potential benefits and applications of psychedelics as medicines, relatively little has been written about the challenges this field will face when incorporated into modern medical practice. Indeed, as a new or at least revived area of investigation, psychedelic medicine has a particular set of challenges which need to be addressed. In this viewpoint, we identify a number of these challenges. First, challenges related to the design of individual research studies are discussed, particularly focusing on current practices surrounding blinding, expectancy, the use of therapy and sources of bias. Second, the broader context of the research environment is considered, including how medical science typically establishes evidence, funding bodies and the impact of psychedelics being scheduled at odds with their risk profile. Finally, we describe challenges relating to the implementation of psychedelic therapies into modern medicine, considering the social and economic context. Alongside, we provide suggestions for what could be included into current research protocols to mitigate these challenges.