The transition to university can often be challenging for individuals with eating disorders (EDs). As such, there is a need to understand protective factors that optimise people's health during this transition. Researchers using the social identity perspective suggest that group identification and psychological well-being may impact ED symptoms. Yet, these effects have not been demonstrated over time, limiting causal understanding. We address this gap by examining the role of affiliative identity and psychological well-being in lowering ED symptoms over the transition to university. First-year university students diagnosed with an ED or symptoms of an ED participated in a three-wave longitudinal study. An online survey was completed by participants at T1 (N = 281), 4 months later at T2 (N = 101) and 12 months later at T3 (N = 36). Self-report measures were used to assess identification with one's most important group, psychological well-being and ED symptoms. Linear mixed-effect models showed that strength of affiliative identity was a positive predictor of well-being across time. Well-being was also shown to be a negative predictor of ED symptoms across time. Using a longitudinal mediation model, strength of affiliative identity had positive implications for people's psychological well-being which subsequently predicted self-reported ED symptoms. This study provides evidence that affiliative identity may be particularly important for enhancing psychological well-being and in turn reducing ED symptoms during the transition to university.