Objectives: To explore whether a school-based water, sanitation and hygiene programme, which includes group hygiene activities, contributes to the formation of independent handwashing and toothbrushing habits among Filipino children. Methods: In this cluster-randomised trial, twenty primary schools were randomly allocated to the intervention or control arm. Intervention schools received group handwashing facilities and implemented daily group handwashing and toothbrushing activities. A soap use to toilet event ratio was calculated to measure children’s independent handwashing behaviour after toilet use, and dental plaque accumulation on Monday morning was measured as a proxy indicator for children’s independent toothbrushing behaviour at home. Results: Four months after implementation, handwashing and toothbrushing behaviours did not significantly differ between intervention and control schools. The mean soap use in intervention schools and control schools was 0.41 g and 0.30 g per toilet event, respectively (p = 0.637). Compared to baseline, mean plaque scores reduced by 4.2% and 3.5% in intervention and control schools, respectively (p = 0.857). Conclusions: Although health benefits have been established, school-based group handwashing and toothbrushing may not be sufficient to increase children’s uptake of independent hygiene behaviours.