More than an academic learning environment, the school is also a place where young people develop behaviorally, emotionally and cognitively and form positive social relationships. Prejudiced attitudes such as homophobia and misogyny are opposed to educational goals and negatively impact the school climate relational aspect. This research aimed to understand this impact through the relationships between different school climates with less or more prejudiced environments in terms to sexual and gender diversity. To fulfill these goals, we draw a quantitative research design from student responses to two surveys. The first, integrating a larger research on prejudice, provided data on attitudes against sexual and gender diversity in the view of 7th grade students from ten Rio de Janeiro city public schools. From these data, we selected two schools with different positions, Iracema School and Hora da Estrela School, and applied a second questionnaire, this time focused on the entire second segment of elementary school, with questions about the school climate, and more items on prejudice against sexual and gender diversity. Despite geographically close and with socially and culturally similar student configuration, coming from the same neighborhoods, the two schools have markedly significant differences in relation to its school climate and prejudiced views and attitudes: from the established indices, it is concluded that Iracema School students perceive a less positive school climate whereas indicate more prejudiced thoughts against sexual and gender diversity than Hora da Estrela School students. We observed that the prejudiced students’ views regarding sexual and gender diversity are positively associated with good peer relationships and negatively associated with: (i) the perception of respect for diversity by the school community; (ii) the school management role on conflict resolution; (iii) the behavior and the feelings of engagement and belonging at school and (iv) the peer victimization through bullying. It is concluded that a school environment marked by a more positive climate can have, at the same time, less misogynist and homophobic students.