This methods paper describes a new UK-wide citizen science project, the Schools' Air Quality Monitoring for Health and Education (SAMHE) project, which is exploring indoor air quality (IAQ) in schools. Central to the project is a Web App, where school teachers and pupils can see air quality and environmental data from their classroom, learn about the significance of the data that their monitor collects, enter important contextual information to support data analysis by researchers, and are supported to do their own experiments related to air quality. School use of the SAMHE Web App is essential to the project's aims to 1) improve understanding of air quality in schools; 2) empower teachers and pupils to make informed decisions about management of their classroom environment, including ventilation; and 3) support the UK's next generation to think differently about air quality. Therefore, it is critical that the SAMHE Web App was co-designed with schools, to maximise its acceptability within schools, and to ensure that teachers and pupils engage with it. This paper describes the co-design process used within SAMHE, how co-design has helped shape the web app (including overall theme, visualisation of data, and supporting materials), and some lessons learned from the process that will be useful for future software development and citizen science projects with schools.