Objective: This cross-sectional, case-control study aimed to explore the psychodynamic characteristics that influenced adolescents’ mental health during the COVID-19 pandemic. Methods: Personality structure impairments, psychodynamic conflicts, defense styles, and mental health issues were examined using the OPD-Structure- and Conflict-Questionnaires, the Defense Style Questionnaire, and the Patient Health Questionnaire in adolescents before (n = 288) and after (n = 451) the COVID-19 pandemic in Germany. Results: Adolescents with mental health issues exhibited greater impairments in personality structure, more immature defense styles, and higher levels of psychodynamic conflicts both before and after the pandemic onset. Comparisons between pre-pandemic and pandemic samples indicated a lower level of the conflict of taking care of oneself versus being cared for in passive mode among adolescents during the pandemic. In-depth analysis of adolescents with mental health issues from the pandemic group revealed significant associations between personality structure impairments and a maladaptive defense style with somatoform, depressive, anxiety, eating, and alcohol use disorders. Conclusion: The findings provide clinically relevant insights into the psychodynamic factors that contributed to the psychological vulnerability of adolescents during the COVID-19 pandemic. These insights can guide the development of targeted psychodynamic interventions to support adolescents’ mental health in similar future crises.