To develop the full potential and enhance the science skills, mathematical abilities, and English proficiency among Filipino learners, the Department of Education implemented a special program in science, technology, and engineering at the basic education level. The students are taught based on an enhanced science-technology-oriented curriculum to prepare them for college and science, technology, engineering, and mathematics-related careers. Since the focus of this program was on science, technology, mathematics, and research, the inclusion of biotechnology subjects is integral in supporting the learners to develop an interest and aptitude in these fields. This study looked into the challenges that schools and educators face in teaching biotechnology using the qualitative research design, specifically a phenomenological approach. Interviews were conducted to obtain data. A multi-step method was employed when interviewing the 11 public high school science teachers about the challenges they encountered in teaching biotechnology. They were interviewed based on how they teach the subject, their teaching approaches, the depth of their understanding of the subject, and their specific teaching challenges. Results identified five essential themes: (a) Expertise Mismatch, (b) Abstract Nature of the Subject, (c) Deficiency in Foundation Knowledge, (d) Lacking Teaching Strategies, and (e) Lack of Learning Resources. A multi-faceted approach can be adopted to approach these identified challenges proactively. This should encompass (a) improvement in teacher training, (b) curriculum overhauling, (c) provision of essential resources, and (d) implementation of innovative teaching methodologies.