Perceived discrimination is a substantial challenge for immigrant youths trying to adapt to a new home. The present study examined the independent and interactive relations between individual- and school-level variables in determining perceptions of discrimination in ethnic German migrant (Aussiedler) youths from the former Soviet Union. Six hundred forty-three Aussiedler adolescents (M = 15.7 years) from 28 schools across Germany self-reported their orientation toward ingroup relationships, perceived native segregation orientation, and perceived discrimination. Eight hundred fourteen native German adolescents from the same schools reported their negative attitudes about Aussiedler. Natives’ negative attitudes about Aussiedler aggregated by school were used as school-level predictor variable, together with the percentage of Aussiedler students per school. With all variables included in multilevel analyses, the individual-level associations were not significant, but both school-level associations and three cross-level interactions were significant. Aussiedler adolescents reported higher levels of discrimination in schools with higher percentages of Aussiedler students and in schools with more negative attitudes toward Aussiedler. The association between immigrant ingroup orientation and perceived discrimination was stronger in schools with fewer Aussiedler students. The association between perceived native segregation orientation and perceived discrimination was stronger in schools with more Aussiedler students and in schools with more negative attitudes about Aussiedler. The findings indicate the importance of the interaction between individual and contextual variables in understanding the ways in which adolescent immigrants come to perceive discrimination.