It has been suggested that group-level factors affect how perceived indoor air quality (IAQ) is associated with well-being. Therefore, we analysed how student-perceived social climate at the school-level modified the student-level association between student-perceived unpleasant odour/stuffy air and well-being. The well-being indicators were seven self-reported anxiety symptoms (such as nervous, anxious, or on edge) and two somatic symptoms (headache and tiredness). We analysed a representative sample of Finnish school students (N = 678 schools, N = 71,392 students) by using multilevel modelling and testing cross-level interactions. At the studentlevel, both unpleasant odour and perceived stuffy air were significantly but weakly associated with increased anxiety and somatic symptoms. At the school-level, these IAQ indicators were significantly but weakly associated with increased anxiety and moderately with somatic symptoms. Furthermore, a good social climate at the schoollevel modified the student-level association between perceived stuffy air and anxiety symptoms. Those students who reported stuffy air were more anxious if they studied in a school with poor social climate than good social climate. Our results provide robust evidence that group-level factors may differently modify the relationships between different IAQ indicators and components of well-being.