International research has highlighted the relationship between the physical environment of schools and the perceived well-being of different actors in the educational community. Although these studies pointed out a relationship between these variables, there is little research that delves into the nature and quality of this relationship. The present study aimed to analyse the mediating effect of the perception of the physical environment of the classroom (considering aspects such as lighting, acoustics, visibility, size, order, and aesthetic features) on the perception of school climate and subjective well-being of students in state-funded schools in Chile. A total of 19.567 students (48,77% female) between fifth and eighth grade from 425 vulnerable schools in Chile participated. Through a simple statistical mediation model, it was identified that the perception of the physical environment mediates about 50% of the total effect on subjective well-being and school climate (c' = 0.09 (0.01); p < 0.001). There is an urgent need to incorporate indicators and evaluations addressing the perceptions of the infrastructure and physical environment in schools, especially when this has been expressed as an explicit and historical demand of the Chilean student movements. This type of approach, including multiple factors, could favour a more articulated vision of the quality of the educational environment, contributing to the academic and emotional development of students.