Underage patients with Borderline Personality Pathology (BPP) are in need of specialised psychotherapeutic treatment. A handful of these treatments, including Adolescent Identity Treatment (AIT) and Dialectical Behavior Therapy for Adolescents (DBT-A), have been adapted for adolescent patients. Psychotherapy research has shown that the outcome of different psychotherapeutic approaches can be very similar despite conceptual and practical differences between the theoretical models. Therefore, to understand what really works in psychotherapy, it is necessary to investigate the psychotherapeutic process and its effects on the patient. This paper presents a study design for process-outcome research, integrating (1) a classical outcome design, comparing AIT and DBT-A in a non-inferiority trial assessing changes in psychosocial functioning at 12 months after baseline as primary outcome; and (2) a process research design, addressing multiple BPP and psychotherapy relevant factors. These factors include well-studied generic variables such as the psychotherapeutic alliance, more recent approaches such as video-based identification of significant therapeutic events, as well as more experimental approaches such as psychophysiological markers measured during the therapeutic sessions. The use of repeated measures and the methodological pluralism which includes event and micro-process analyses has been recommended for psychotherapy research aiming at a better understanding of the interplay of factors at work to narrow the gap between research and practice in this field.