Children are in school for one-third of their normal day where bad indoor air quality (IAQ) emerges as a real problem. As in most countries, schools in Portugal are not subject to regular monitoring of IAQ and its health effects. STEP has Estarreja as a case study, and aims to answer the following 3 main questions: What causes air pollution in and around schools? What are the effects? What are the possible solutions to tackle it? A citizen-science initiative to monitor indoor and outdoor air quality in and around primary and kindergarten school classrooms is proposed, involving multipollutant monitoring and the application, for the first time, of new disciplines, such as analytical toxicology, microbial genomics, and occupational epidemiology. In addition to regulated pollutants and comfort parameters, a bioburden assessment will be done, including the detection of toxigenic fungi and antimicrobial-resistance genes. Dust will be chemically characterised and subject to a toxicological screening to obtain stressor-response patterns. A cross-sectional study in which pupils will be diagnosed by means of the International Study of Asthma and Allergies in Childhood (ISAAC) questionnaire will be conducted to estimate the burden and risk factors of diseases. Multivariate models will be applied to search for associations between air quality, respiratory health, and absenteeism. A dosimetry model will be used for risk assessment and development of occupational exposure limits for inhaled particles. A set of guidelines and good practices will be proposed for effective IAQ management and behavioural changes towards a healthy school environment.