Abstract Background Children and adolescents spend a lot of time sitting at school. Implementing standing desks in the classroom is one potential strategy to reduce and break up sitting time. The first aim was to evaluate the effect of implementing standing desks in classrooms in primary and secondary schools on pupils’ sitting-related behaviour and determinants. The second aim was to quantitatively and qualitatively evaluate the process of implementing the desks in the classroom. Methods We conducted a cluster-randomised controlled trial with a pre-, mid-, and post-test design including 10 intervention schools (5 primary, 5 secondary schools) and 9 control schools (5 primary, 4 secondary schools) across Flanders, Belgium. Three standing desks were placed in one class in each intervention school for 6 months. At pre-, mid- and post-test, all pupils (n = 311; 54.5% girls) completed a questionnaire whilst a subsample of three pupils per class wore an activPAL inclinometer for one school week. Focus groups with ...