Background: Borderline personality disorder (BPD) and substance use disorders (SUD) are frequently co-morbid and their co-occurrence exacerbates the symptomatology and associated harms for both disorders. However, few intervention studies have examined the delivery of an integrated intervention for BPD and SUD within alcohol and other drug (AOD) treatment settings. This single arm pilot study examined the clinical utility and outcomes of a 12-session emotion regulation intervention for clients with co-occurring SUD and BPD symptoms delivered in an outpatient AOD treatment setting. Method: Forty-five adult treatment-seekers (64.4% women, mean age 35.8 years (SD = 10.4)) attending an outpatient AOD service, who exhibited three or more symptoms of BPD, engaged in a 12-session emotion regulation intervention. Clinical measures assessing alcohol and drug use, BPD symptoms, emotion dysregulation and acceptance, non-avoidance of thoughts and emotions, and psychological flexibility were collected at baseline, session 6 and session 12. Treatment engagement, satisfaction, and rapport were also measured. Results: Fifty-one percent of participants completed the 12-session intervention. The results demonstrated that the number of drugs using occasions in the past 28 days significantly reduced from baseline compared to session 12. Furthermore, a significant reduction was identified in BPD symptom severity, emotion dysregulation, and non-acceptance, experiential avoidance, and psychological inflexibility from baseline to session 12. Conclusions: For those individuals who completed the 12-session emotion regulation intervention, there were significant reductions across a number of clinical outcomes. However, retention in treatment for this vulnerable client group remains a significant challenge in the AOD setting.