Background: The high rates of attrition in STEM (science, technology, engineering and mathematics) programmes causes concern over a future shortage of graduates entering STEM careers. Students’ first year experiences critically affect their motivation and are therefore also critical components of students’ academic success in terms of retention, learning and subsequent performance. Purpose: This study explores STEM students’ encounters with an interdisciplinary first year. Specifically, motivational patterns towards learning in two introductory courses followed by students from multiple study programmes are investigated. Sample: 173 Danish undergraduate students enrolled in three science programmes: biomedicine; biochemistry and molecular biology; and physics. Design and methods: Within the framework of Self-Determination Theory, a measure of autonomous and controlled motivation forms the basis for quantitative analyses (n = 173). A qualitative thematic analysis of students’ open responses further supplements and gives nuance to the findings. Results: The motivational pattern of physics students is found to differ significantly from that of biochemistry and molecular biology (BMB) students and biomedicine students. The comments reveal that some students struggle to realise the relevance of the course content for their chosen study programme to an extent that makes them reconsider their study choice. Conclusions: The study offers input to the discussion of how to present inter- and/or multidisciplinarity to students and points to implications on two levels: curriculum design and course content. The findings are of importance to educational planners, decision-makers and teachers dealing with the motivational range that exists within their courses.