Schools, as community facilities, play a significant role in the transmission of SARS-CoV-2 and influenza. Keeping schools open during a pandemic is a crucial societal objective. Therefore, understanding how respiratory viruses spread in schools and their effects on children’s emotional well-being is essential. In secondary school classrooms, biomedical measurements (such as indoor carbon dioxide levels, relative humidity, particles, and viral genetic material in the air) are taken, along with data on students’ well-being and emotional experiences. Two study periods, each lasting seven weeks, were conducted from January to March 2022 and from January to March 2023. A follow-up study focusing on transmission of respiratory viruses and spatial movement of pupils data took place in the first half of 2024.