Individuals with mild intellectual disabilities or borderline intellectual functioning are at increased risk to develop a substance use disorder—however, effective treatment programs adapted to this target group are scarce. This study evaluated the effectiveness of Take it Personal!+ in individuals with mild intellectual disabilities or borderline intellectual functioning and substance use disorder. Take it Personal!+ is a personalized treatment based on motivational interviewing and cognitive-behavioral therapy supported by an mHealth application. Data were collected in a nonconcurrent multiple baseline single-case experimental design across individuals with four phases (i.e., baseline, treatment, posttreatment, and follow-up). Twelve participants were randomly allocated to baseline lengths varying between 7 and 11 days. Substance use quantity was assessed during baseline, treatment, and posttreatment with a daily survey using a mobile application. Visual analysis was supported with statistical analysis of the daily surveys by calculating three effect size measures in 10 participants (two participants were excluded from this analysis due to a compliance rate below 50%). Secondary, substance use severity was assessed with standardized questionnaires at baseline, posttreatment, and follow-up and analyzed by calculating the Reliable Change Index. Based on visual analysis of the daily surveys, 10 out of 12 participants showed a decrease in mean substance use quantity from baseline to treatment and, if posttreatment data were available, to posttreatment. Statistical analysis showed an effect of Take it Personal!+ in terms of a decrease in daily substance use in 8 of 10 participants from baseline to treatment and if posttreatment data were available, also to posttreatment. In addition, data of the standardized questionnaires showed a decrease in substance use severity in 8 of 12 participants. These results support the effectiveness of Take it Personal!+ in decreasing substance use in individuals with mild intellectual disabilities or borderline intellectual functioning.