Due to rising Islamophobia in Europe today, Muslim ethnic minority adolescents are at great risk of experiencing identity-based harassment at school. We extend previous research on ethnic discrimination by focusing on religious discrimination of Muslim adolescents and its effect on their psychological (i.e., depressive symptoms and self-esteem) and behavioural adjustment (i.e., disruptive behaviour at school). Further, we consider Muslim adolescents' ethnic and religious identification as two factors that may promote adolescents' adjustment and protect them from the negative consequences of discrimination. We used data from N = 105 Muslim ethnic minority adolescents (M[subscript age]= 13.30, SD = 0.75, 45% female). Factor analysis revealed that adolescents did not differentiate between ethnic and religious discrimination. Results show that higher perceived ethno-religious discrimination (PERD) was related to more depressive symptoms. While higher ethnic identification was associated with greater self-esteem, higher religious identification was related to fewer depressive symptoms. Contrary to our expectation, Muslim adolescents who were highly identified with their ethnic group reported more depressive symptoms when experiencing more PERD. Their self-esteem was negatively affected by higher PERD when possessing high religious identification, while for low religious identification a positive effect of higher PERD on self-esteem emerged. Results highlight the importance of developing evidence-based intervention programmes for schools to tackle identity-based harassment.