Organic chemistry, also known as stereochemistry, is a subject considered to be notably complex for students to understand. Knowledge construction in stereochemistry might demand the ability to imagine or visualise the distribution of atoms. For students with insufficient spatial ability, this could be confusing. This study aimed to explore empirically students and teachers’ experiences regarding the opportunities and challenges they encountered when using virtual reality (VR) and augmented reality (AR) technologies to teach and learn stereochemistry, as well as how these technologies might support students’ spatial ability and 21st-century skills in K-12 education by participating in virtual lab environments. Using design-based research methods, an exploratory study based on the utilization of immersive technologies was designed and carried out with three groups in Grade 8. Two researchers observed the activities that were implemented, after which the participating students answered a qualitative survey about how these technologies and the specific teaching design might support their understanding of molecules in 3D space. The schoolteacher was interviewed afterwards, and she shared her motives and goals (e.g., what she sought to achieve) by using the technologies in her teaching. The results show that the students had a positive experience in their learning of chemistry through immersive realities, increased motivation to learn the subject, and their test results improved slightly. However, it is essential for a teacher to possess technological know-how regarding VR and AR to achieve the intended goals. The findings highlight the added value of these immersive technologies by enhancing students’ learning processes and the central role of the teacher as a designer and technological leader of the group.