Response rates in epidemiological studies have generally been decreasing over the past decades. However, when the target group consists of adolescents and young adults, school-based surveys have hitherto been able to mitigate this problem: This age group can be reached relatively easy in the school context (e.g., as compared to reaching them by phone) with very low refusal rates at the student level. However, the present study used a mixed-methods approach and suggests that schools at the organizational level have meanwhile become the problematic bottleneck for school-based surveys, as they increasingly reject requests for study participation. The current article provides insights into promising means for counteracting this trend. Researchers are advised to offer flexible timeframes for schools’ participation and to involve institutional gatekeepers who are endorsing their study. Furthermore, researchers, funding agencies, and schools would benefit from joint regional survey coordination systems. Such means will be crucial for the representativeness of future school-based epidemiological surveys.