Introduction Exposure to poor environmental conditions has been associated with deterioration of physical and mental health, and with reduction of cognitive performance. Environmental conditions may also influence cognitive development of children, but epidemiological evidence is scant. In developed countries, children spend 930 hours per year in a classroom, second only to time spent in their bedroom. Using continuous sensing technology, we investigate the relationship between indoor environmental quality (IEQ) and cognitive performance of school-aged children. The proposed study will result in a better understanding of the effects of environmental characteristics on cognitive performance, thereby paving the way for experimental studies.Methods and analysis A study protocol is presented to reliably measure IEQ in schools. We will monitor the IEQ of 280 classrooms for 5 years, covering approximately 10 000 children. Each classroom in the sample is permanently equipped with a sensor measuring air quality (carbon dioxide and coarse particles), temperature, relative humidity, light intensity and noise levels, all at 1 min intervals. The location of sensing equipment within and across rooms has been validated by a pilot study. Academic performance of school-aged children is measured through standardised cognitive tests. In addition, a series of health indicators is collected (eg, school absence and demand for healthcare), together with an extensive set of sociodemographic characteristics (eg, parental income, education, occupational status).Ethics and dissemination Medical Ethical Approval for the current study was waived by the Medical Ethical Committee azM/UM (METC 2018-0681). In addition, data on student performance and health stems from an already existing data infrastructure that are granted with ethical approval by the Ethical Review Committee Inner City faculties (ERCIC_092_12_07_2018). Health data are obtained from the ‘The Healthy Primary School of the Future’ (HPSF) project. Medical Ethical Approval for HPSF was waived by the Medical Ethical Committee of Zuyderland, Heerlen (METC 14 N-142). The HPSF study protocol was registered in the database ClinicalTrials.gov on 14-06-2016 with reference number NCT02800616, this study is currently in the Results stage. Data collection from Gemeentelijke Gezondheidsdienst Zuid-Limburg (GGD-ZL) is executed by researchers of HPSF, this procedure has been fully approved by the Medical Ethical Committee of Zuyderland. The questionnaires on level of comfort will be filled in anonymously by students and teachers. The study will follow the EU General Data Protection Regulation (EU GDPR) and Dutch data protection law to ensure protection of personal data, as well as maintain proper data management and anonymisation.The protocol discussed in this paper includes significant efforts focused on integrating results and making them available to both the scientific community and the wider public, including policy makers. The results will lead to multiple scientific articles that will be disseminated through peer-reviewed international journals, as well as through conference presentations. In addition, we will exploit ongoing collaboration with project stakeholders and project partners to disseminate information to the target audience. For example, the results will be presented to school boards in the Netherlands, through engagement with the Coalition for Green Schools, as well as to school boards in USA, through engagement with the Center for Green Schools.Trial registration number NCT02800616; Results.