Despite national policies, de facto school segregation for racial/ethnic minority students in the West and East has continued to deepen. In Hong Kong, the segregated school system was abolished in 2013, while from 2004 reformed School Places Allocation Systems encouraged minority students to choose mainstream primary and secondary schools. However, de facto ethnicity-based school segregation continues to prevail. Most minority students in the mainstream system are stuck in low-status schools where they face discrimination and institutional exclusion. This has led many of them to retreat to a limited number of schools that have traditionally catered for minority communities. Such segregation calls forth scholarly attention to the paradoxical correlation between the physical mixing of diverse students and equality of educational opportunity, especially equal access to post-secondary education (PSE)—a key for minority youth to function in the competitive labour market. This study employed the theory of school-based social capital (SBSC) and compared the ways in which PSE-relevant institutional resources and support were rationalised and enacted by staff in de facto segregated and desegregated school contexts. Case studies of two secondary schools lead us to argue that desegregation is only effective when institutional structure, culture and agents empower minority students through access to instrumental resources and support for the pursuit of PSE. The findings confound the desegregation policy and call for structural/institutional interventions to ensure instrumental SBSC is accessible to PSE-bound minority students in all schools, and thus increase the effectiveness of school desegregation. Copyright © 2023 British Educational Research Association.