The aim of the study was to examine how the psychological, cognitive and social dimensions of well-being were constructed regarding Swedish Grade 6 pupils’ school experiences, and whether the three constructs differed between pupils. In 2011, major educational reforms were implemented in the Swedish school system, which resulted in earlier introduction of grades (in 6th Grade), which overall created a stricter high-stakes assessment system. In the study, the educational reforms were used to investigate implications on pupils’ school-related psychological, cognitive and social well-being, by comparing two cohorts of pupils born 1998 (did not experience reform) and pupils born 2004 (experienced full reform). The additional variables were sex, educational background and cognitive ability. Data were retrieved from the longitudinal project Evaluation Through Follow-Up. Confirmatory factor analysis and structural equation modeling were used. The results supported the theoretical construction of measurement instruments for psychological, cognitive and social well-being. Further, the results indicate that the reforms affected pupils’ psychological and social well-being negatively. Girls reported lower psychological well-being compared to boys, while pupils’ cognitive ability had particularly strong effects on psychological and cognitive well-being. Generally, the effects were stronger for the 2004 cohort.