This longitudinal study examined school engagement and burnout profiles among early and middle adolescents before and during COVID‐19, and within‐class latent change and stability in students’ socio‐emotional skills the profiles. The longitudinal data were collected in fall 2019 and 2020 from 1381 5th to 6th, and 1374 7th to 8th grade students. Using repeated measures latent profile analyses based on school engagement and burnout we identified five study well‐being change profiles in both samples showing structural similarity: normative (53% sample 1; 69% sample 2), moderate‐decreasing (4%; 5%), high‐decreasing (17%; 10%), low‐increasing (6%;7%) and moderate‐increasing (20%; 10%) groups. The groups with increasing study well‐being showed simultaneous increase in intrapersonal socio‐emotional competencies but showed less changes in interpersonal outcomes.