The exploration of threshold concepts, which represent a transformed way of understanding, interpreting, or viewing something necessary for a learner’s progress, has significantly influenced teaching and learning in higher education, gaining broad acceptance in academic circles. Despite widespread enthusiasm, the scientific development of the field faces obstacles, especially epistemological and ontological uncertainties, directly implying the reliability of identification techniques and, by extension, raising questions about the validity of previous findings. This comprehensive review delves into 60 articles sourced from the Web of Science database to scrutinize the literature on threshold concept identification. The findings confirm the adaptability of threshold concepts across diverse disciplines. However, the fluid definition inherent in these concepts introduces ontological challenges, influencing biases in the identification process. The review highlights the diverse identification methods influenced by knowledge area specificities, community affinities, and research practice traditions. A diagram depicting the methods employed to identify threshold concepts is offered to highlight five central decisions to be considered. Acknowledging professors as pivotal mediators adept at navigating the epistemological and ontological dimensions of threshold concepts while integrating theoretical and applied knowledge, this study enhances our nuanced understanding of threshold concept identification. Emphasizing methodological validity and reliability, it acknowledges the crucial role of experienced educators in this issue and presents future perspectives for advancing current research, fostering the maturation of the field.