This study examined changes in student well-being and its relationship with academic performance, in light of concerns about rising inequalities caused by the COVID-19 pandemic. It utilized PISA student surveys and reading and math assessments from 2018 and 2022 (N = 33,147) among 15-year-old adolescents from Finland, Sweden, and Iceland. Adopting a person-centred approach, the study aimed to identify distinct well-being profiles based on their school attendance, life satisfaction, and sense of school belonging. Four well-being profiles were identified in both cohorts: High Well-being, Moderate Well-being, Present but Disconnected, and Disengaged. Unexpectedly, the proportions of students within each profile remained stable over time. Lower socioeconomic status (SES) was consistently associated with less favourable well-being profiles, though the interaction between SES and cohort was not significant, indicating persistent but not worsening disparities. Academic performance declined across all profiles, with smaller losses observed among students with lower well-being, suggesting a slight levelling effect. The association of SES and academic performance intensified only within the High and Moderate Well-being profiles. Mediation analysis indicated that well-being had a minimal impact on the relationship between SES and academic performance, with no increase in the mediation effect over time. In conclusion, the study challenges the prevailing narrative that the pandemic exacerbated educational disparities related to well-being. Instead, it shows a pattern of stability and modest levelling in academic outcomes across well-being profiles. This research contributes to ongoing discussion on students' academic well-being and socio-educational inequalities in the post-pandemic era.