Research shows that religious identity is associated with health. The aim of this study was to understand the role of religious identity for refugee minors’ health in greater detail. Middle Eastern refugee minors resettled in Germany and aged 8–18 years completed questionnaires at baseline (T1, n = 246) and follow-up (T2, n = 122) measurement between 2019 and 2022. Religious identity was assessed with a 4-item measure (Cronbach’s α = .89). Associations of religious identity at T1 with health-related quality of life (HRQoL) at T1, change in HRQoL from T1 to T2, and perceived COVID-related stress at T2, as well as the mediating role of resources were examined. The results showed a positive association between religious identity and HRQoL, which was partially mediated by integration into peer group, but not by ethnic identity, sense of coherence or religious practice. No significant associations between religious identity and change in HRQoL or COVID-related stress occurred. Therefore, cross-sectional analyses support the beneficial role of religious identity for HRQoL and the crucial mediating role of integration into peer group, suggesting the promotion of religious identity or peer group integration. However, the absence of significant effects on change in HRQoL from T1 to T2 and COVID-related stress at T2 do not allow drawing any long-term conclusions.