The aim of this study is to explore whether and how school-based social capital (SSC) may increase or reduce inequalities in the academic achievement and well-being of students from different backgrounds (class, gender, and ethnicity). SSC here refers to those qualities of social relationships and the degree of interconnectedness between students, teachers, and parents that can support the educational attainment and social adjustment of young people. As the results of our ethnographic studies indicate, there is a significant association between SSC and school composition—i.e., the class and ethnic background of students in a school. The association indicates the stratification effect of social capital in schools as a predominant pattern. In a school with students from higher socio-economic backgrounds, we observed more qualified and motivated teachers, an intensive parental involvement, and, consequently, more constructive and friendly relationships among students. In contrast, in a school located in a disadvantaged area, the social relations were quite the reverse. We then found a third category. In a school with children from lower social class backgrounds placed in an immigrant-dense area, highly committed school staff were able to create an emotional closeness and trust between them, the pupils, and their parents. School-based social capital in this context introduced a sense of solidarity and created a pro-educational climate.