Most research has so far focused primarily on the negative effects of the COVID-19 pandemic on early adolescents. This pre-registered study fills this gap by investigating possible links between pandemic regulations and positive outcomes, namely school well-being. Specifically, we test the assumption that high-ability early adolescents benefit from virtual schooling by experiencing higher school well-being while schooled virtually. Data from a Czech sample (N = 210) do not support this claim but show a strong effect of autonomy on school well-being. We also explore the changes reported by our participants after returning to classrooms.