Background: Anxiety disorders, depression, and borderline personality disorder often emerge during adolescence, yet early psychiatric assessment remains challenging because conventional interviews are subjective, clinician-dependent, and difficult to scale. Digital phenotyping may improve early identification by combining standardized digital interviews with multimodal behavioral, linguistic, physiological, and environmental markers. Methods: An observational cross-sectional study with a 2 × 4 design with random allocation to interview mode. Adolescents and young adults aged 12–20 years with anxiety disorders, depressive disorders, borderline personality disorder, and controls will complete one standardized pre-screening interview using either a text-based chatbot or a virtual agent on a tablet device at the University Medical Centre Maribor, Slovenia. During a single visit, participants complete a battery of standardized questionnaires, undergo audio-video recording, contactless physiological monitoring, and indoor air-quality sensing. Primary outcomes are participant-reported acceptability measures. Secondary analyses will test effects of interview mode and diagnostic group, and exploratory analyses will examine associations between symptom dimensions and multimodal digital markers. The planned sample size is 120–240 participants. Discussion: The study will assess acceptability of chatbot- and virtual-agent-delivered pre-screening interviews in youth mental health and create a clinically annotated multimodal dataset for future digital phenotyping research. The dataset is intended to support subsequent development of explainable artificial intelligence models and privacy-preserving synthetic data for adolescent mental health research. The findings may also provide evidence on the clinical utility of these interview formats as complementary, scalable tools for early detection and triage in adolescent mental health settings. Trial registration: The study was registered in the ISRCTN registry (on 9 March 2026, ISRCTN55639530). The study was approved by the National Medical Ethics Committee of the Republic of Slovenia (on 13 October 2025, ref. 0120-466/2025-2711-3). Written informed consent will be obtained from all participants, with parental or guardian consent and minor assent obtained where applicable.