To account for the disruption brought about by the COVID-19 crisis, this paper explores its impact on students’ pathways after compulsory education, as this transition is a key step in the Swiss schooling system. As in most European countries, foreign and/or migrant students in Switzerland are more likely to experience non-linear school trajectories which can negatively affect their educational access and professional opportunities. The effect of immigration backgrounds on the transition from lower to upper secondary school is thus thoroughly assessed. We further explore whether the inequalities faced by pupils with a migrant background were strengthened by the COVID-19 crisis as they were with previous societal, systemic, or cyclical crisis. Using administrative data, we study educational pathways over 2 years, starting from the end of mandatory school. Relying on a typology of these trajectories, we compare and describe the differences between three cohorts who completed their compulsory schooling in the spring of 2017, 2019 and 2020. Results show that pupils favour institutional options in times of crisis and an overall stability of the VET system. We find evidence of migrations background effects, with strong differences amongst foreign nationalities and residency permits. This study contributes to understanding the diversity migration backgrounds and offers insight into the persistent disadvantages that afflict certain minorities.