Background Children and adolescents with intellectual disabilities (ID) are at increased risk of developing challenging behaviour. Challenging behaviour may be partially explained by low individual communicative competences. However, communication involves at least two partners, thus outcomes may also vary according to each interaction partners' abilities. We therefore investigated the degree to which the interplay between individual and classmates' communication skills predicts changes in challenging behaviour among students with ID. Methods This study used a longitudinal design with two measurement points across one school year. Challenging behaviour and communication skills were measured by teacher reports in 1125 students with ID attending special needs schools. Applying a multilevel approach, we investigated (1) whether higher individual communication skills at the first measurement were related to a subsequent decrease in challenging behaviour and (2) whether this effect was moderated by classmates' levels of communication skills. In addition, we examined (3) if classroom communication skills were indirectly related to a decrease in challenging behaviour by influencing individual communicative abilities. Results Higher individual communication skills at the first measurement were significantly related to a decrease in general challenging behaviour over the school year. This effect was not moderated by classroom-level communication skills. However, classmates' communication skills exerted an indirect influence by enhancing individual communicative abilities. Further analyses suggested classroom contextual effects related to a decrease in several sub-domains of challenging behaviour. Conclusions The study results suggest that both individual communicative competences and those of the classroom context are relevant to understanding challenging behaviour development in ID. Perspectives for counteracting such behaviour in light of the present findings are discussed.