Higher engineering education programmes increasingly include courses characterised by real-world problems and student collaboration in multidisciplinary teams. Research findings demonstrate that students remain limited in perceiving and meaningfully bridging disciplinary differences in these course contexts. Drawing on the literature on boundaries and boundary interactions, this study sought to investigate how applied physics and mechanical engineering students managed their disciplinary differences in a challenge-based learning course. Using a qualitative, case study methodology, data from two multidisciplinary student teams (n = 12) were collected through reflective journals, individual interviews, and observations of team meetings. The findings confirm the value of disciplinary boundaries in creating new learning opportunities. The students coordinated their disciplinary differences during discussions in team meetings, preparations for the project plan and the stakeholder pitch, and test sessions in the lab. Results provide insights for designing similar courses and for future research.