In this paper, we aim to understand the implications of the structural changes of the Bologna process from a student perspective. We investigate how bachelor’s degree students’ in a post-Bologna era with three-year bachelor’s degree and two-year master’s degree units construct their post-bachelor’s choice narratives in two different science degree programmes (chemistry and natural resources) at a Danish research-intensive university. We pay special attention to how science students’ narrative repertoires and imagined futures interact with and set the scene for their choice narratives in specific disciplinary settings. We draw on theoretical ideas of science identities including ‘narrative repertories’ and ‘imagined futures’, combined with disciplinary cultures and institutional capital. The analysis draws on small-scale rich qualitative material including 12 narrative interviews and focus groups with 44 students, including reflective essays, drawings and word-cloud brainstorms. Results show that the post-bachelor’s trajectory is a choice that students must relate themselves to in their identity negotiations. We document how students within the same faculty are presented with different narrative repertoires to construct and negotiate their choices from and as a result experience different choice processes and negotiations due to the different disciplinary settings they encounter. The implications for higher education institutions are given.