While the field of psychedelic research is continuously expanding and offers new hope for achieving successful treatments for physical and mental disorders, certain methodological aspects require improvement. Some of the flaws are shared with clinical trials for other kinds of drugs and others are specific to the field. Given that psychedelic research is an emerging field, it is important to address these problems in a timely manner. In this manuscript, we present the main methodological issues in psychedelic research, ranging from the most manageable (e.g., non-representative samples) to the most complex (e.g., limitations of the biomedical model). In addition, given its relevance, we dedicate a section of the manuscript to a discussion of ethical concerns around psychedelic research.