Introduction During a health crisis, hospitals must prioritise activities and resources, which can compromise clerkship-based learning. We explored how health crises affect clinical clerkships using the COVID-19 pandemic as an example. Methods In a constructivist qualitative study, we conducted 22 semi-structured interviews with key stakeholders (i.e. medical students and doctors) from two teaching hospitals and 10 different departments. We used thematic analysis to investigate our data and used stakeholder theory as a sensitising concept. Results We identified three themes: (1) emotional triggers and reactions; (2) negotiation of legitimacy; and (3) building resilience. Our results suggest that the health crisis accentuated already existing problems in clerkships, such as students' feelings of low legitimacy, constant negotiation of roles, inconsistencies navigating rules and regulations and low levels of active participation. Medical students and doctors adapted to the new organisational demands by developing increased resilience. Students responded by reaching out for guidance and acceptance to remain relevant in the clinical clerkships. Doctors developed a behaviour of closing in and focused on managing themselves and their patients. This created tension between these two stakeholder groups. Conclusion A health crisis can critically disrupt the hierarchical structure within the clinical clerkships and exacerbate existing conflicts between stakeholder groups. When medical students are not perceived as legitimate stakeholders in clinical clerkships during a health crisis, their attendance is perceived as unnecessary or even a nuisance. Despite increased student proactiveness and resilience, their roles inevitably shift from being doctors-to-be to students-to-be-managed.