Previous literature shows that university students are particularly vulnerable to psychological ill-being. Also throughout the COVID-19 pandemic, stressors ranging from uncertainty to disruption of social lives have influenced their well-being. Resilience as a psychological resource could help students deal with such crises. Furthermore, students’ learning environment can substantially determine their well-being and resilience, by satisfying their basic psychological needs for autonomy, competence, and relatedness. The present study aims to longitudinally investigate students’ well-being and resilience in relation to their learning environment. To this end, we interviewed six participants, of which two were university students, two university teachers, one study advisor, and one student psychologist. With a longitudinal interview study with four dates of measurement, spanning the pre to mid-COVID-19 pandemic period, we gathered commentary about the evolution of student well-being, resilience factors, and the effects of the learning environment. To analyse the interview data, we used thematic inductive and deductive coding. The participants confirmed the postulated stressors, but also positive consequences for student well-being, including resilience growth. Interviewees also reported a variety of resilience factors, both within the individual (e.g. social support) and within academia (e.g., impaired student-teacher relationship, diminished sense of belonging). Furthermore, the interview data indicate changes in teaching related to students’ needs for autonomy, competence, and relatedness, which in turn have consequences for learning and engagement, including challenges, opportunities, and positive outcomes. These findings, connecting the learning environment to student well-being and resilience, may help reshape academic systems for the post-pandemic future.