This study investigates whether the ethnic and socioeconomic composition of the secondary school affect higher education enrollment and program choice (non-university higher education or university) in an educational system using a separation model. School-wide social capital is investigated as an underlying mechanism to explain how school composition affects higher education enrollment. Results of logistic multilevel analyses, carried out on the International Study of City Youth (ISCY) data of 1131 Flemish students across 30 schools, demonstrated that students enrolled in migrant concentration schools showed lower rates of higher education attendance because these schools were associated with a low socioeconomic composition. Attending high migrant composition schools and/or high socioeconomic composition schools was beneficial to attend university programs. High-quality peer relationships mediated these composition effects. Additionally, a boosting effect of teacher-student relationships and a buffering effect of high-quality peer relations at school were found, rendering these interesting tools for educational policy makers to decrease social inequality in higher education enrollment and program choice.