Background: Owing to methodological issues, little research has been conducted to examine quality of life (QoL) as a treatment outcome in autism spectrum disorders (ASD) and intellectual disabilities (ID). This study was conducted to combine QoL measures and objective observations of challenging behaviours (CB) in order to evaluate changes over time in adults with ASD and ID who were treated in two different residential programmes; we hypothesised that a decrease in CB would be related to an improved QoL. Method: In a longitudinal study (45 months), we followed 31 adults with ASD and ID who had been integrated into two residential programmes [Autism Programme with a Structured Method (PAMS) vs. traditional programme for ID (No-PAMS)] for 2-19 years. QoL [Quality of Life Inventory in a Residential Environment (IQVMR)] and severity of autistic features (Childhood Autism Rating Scales) were evaluated annually. CB, as measured by the Aberrant Behaviour Checklist (ABC), including stereotypic behaviour and inappropriate speech, were repeatedly assessed every 3 months. Results: Observed separately, the groups' results were different. In the PAMS programme, stereotypic behaviour and inappropriate speech (ABC scores) significantly decreased, and the IQVMR total score increased; in contrast, in the comparison group, ABC scores did not change and the IQVMR total score decreased. In all, three mixed-effect ANCOVAs partially confirmed that the PAMS programme had an effect on CB and that QoL improvement did not directly depend on the type of programme but on reducing CB as measured by the ABC. Conclusion: The PAMS programme has a positive and indirect influence on QoL by reducing CB.