Increasingly, sustainability challenges in transdisciplinary courses are used to confront students with different dimensions of uncertainty, such as unpredictability, lack of knowledge, or ambiguity. However, little is known about how teachers adapt their teaching to scaffold students through such uncertainty. This design-based study investigates the adaptive guidance (scaffolding) employed by teachers to guide students through problem-solving in uncertainty. Using a sixteen-week challenge-based learning (CBL) course called the ‘Living Lab’ as a case study, we monitored how teachers developed scaffolding based on a workshop they received before the course began. Through qualitative questionnaires and focus groups conducted every four weeks, teachers reflected on their teaching practices and coaching strategies. The study identifies teaching problems faced by teachers in transdisciplinary courses, including theoretical grounding, tensions with the commissioner, and assignment clarity. Teachers most frequently used scaffolding for frustration control, marking critical features, and direction maintenance. Additionally, teachers lacked diagnostic strategies to assess student progress on personal learning objectives. This research contributes to a deeper understanding of the role of teachers as coaches in transdisciplinary courses. Practical implications include informing and inspiring teachers to enhance their scaffolding practices on diagnostics, theoretical grounding, and personal learning in CBL courses.