The quality of education suffers when pedagogies are not aligned with physical learning spaces. For example, the architecture of the triple-decker Victorian schools across England fits the information transmission model that was dominant in the industrial age, but makes it more difficult to implement student-centred pedagogies that better fit a modern knowledge society. Yet, very little is known about how to reach powerful alignment of pedagogies and physical learning spaces. This article aims to fill this gap by describing a participatory design process to help to realise physical spaces and school buildings that optimally support specific visions of learning and pedagogy. Three phases are distinguished in this design process: (1) specifying the pedagogy, (2) aligning the pedagogy with seating arrangements and physical learning spaces, and (3) realising the school building. Particular attention is given to the core tasks relating to pedagogy (phases one and two), and especially the second phase, in which school management, teachers and students on the one hand, and architects and interior designers on the other must collaborate in a participatory design process. Illustrations are given from two schools, UCL Academy in London, UK, and De Werkplaats Kindergemeenschap in Bilthoven, The Netherlands.