Background: Atypical sensory processing often impairs the emotional and behavioural functioning and social participation of autistic individuals. However, evidence lacks on the effect of cognitive abilities. Therefore, the aim of this study was to examine the moderating effect of cognitive abilities on both associations. Method: We studied 241 individuals with Autism Spectrum Disorder (ASD) with varying cognitive abilities (mean age: 15.1 years, range: 5.1 to 54.1; IQ < 40 to > 130), using standardized questionnaires on sensory, emotional and behavioural functioning and social participation. Multiple linear regression analyses were performed to investigate the moderation effects. Results: Individuals with higher cognitive abilities showed relatively more emotional and behavioural problems when reporting more sensory processing problems compared to autistic individuals having lower cognitive abilities (beta = -.29, p =.004). No significant effect occurred for social participation. Conclusions: Cognitive abilities moderated the association of atypical sensory processing with emotional and behavioural problems, but not with social participation. In particular, higher cognitive abilities were associated with more problems. This may imply that cognitive abilities should be accounted for in the provision of care to autistic individuals.