|Alcohol, cannabis or other illicit drug use by youth with mild intellectual disability or borderline intellectual functioning is more likely to become substance use disorder than for youth of average intelligence. Daily diary sampling is used to assess substance use patterns of these at-risk youth. We first assess this method’s feasibility for the target group and then explore dynamic substance use patterns and complex interactions with affect, behaviour and context at the individual and group level. An existing personality-tailored prevention programme is further developed, o.a. by integrating it with daily diary sampling. The programme’s effectiveness in decreasing substance use is assessed in a multiple baseline design trial. We use complex systems theory as a framework to analyse the daily diaries, and—combined with qualitative components—examine in-depth how and why idiosyncratic change occurs.