Bronfenbrenner's ecological model postulates the home and school to be key microsystems in fostering emotional well-being and school functioning in children. Utilizing a sample of 663 Filipino American adolescents who participated in the Children of Immigrants Longitudinal Study (CILS), we assessed the effect of intergenerational conflict at home and racial discrimination at school on their mental health and academic achievement. Cross-sectionally, intergenerational conflict and school-based racial discrimination increased depression and decreased academic achievement in early adolescence. Longitudinally, conflict and discrimination in early adolescence decreased academic performance while conflict alone increased depression in late adolescence. Implications of the findings were discussed.