Childhood maltreatment and mental health problems are common among young people placed out-of-home. However, evidence on the impact of maltreatment on the course of mental health problems in at-risk populations is sparse. The aim of this longitudinal study is twofold: (a) describe the course of mental health problems and the shift in symptom patterns among adolescents in youth residential care into young adulthood and (b) assess how childhood maltreatment is related to the course of mental health problems. One hundred and sixty-six adolescents in Swiss youth residential care were followed up into young adulthood (36.1% women; MAge-Baseline = 16.1 years; MAge-Follow-Up = 26.4 years). Latent transition analysis was employed to analyze transitions of symptom patterns and their association with maltreatment exposure. We found three latent classes of mental health problems: a “multiproblem”-class (51.8% baseline; 33.7% follow-up), a “low symptom”-class (39.2% baseline; 60.2% follow-up), and an “externalizing”-class (9.0% baseline; 6.0% follow-up). Individuals in the “multiproblem”-class were likely to transition towards less-complex symptom patterns. Higher severity of self-reported childhood maltreatment was associated with more complex and persistent mental health problems. Our study underlines the need for collaboration between residential and psychiatric care systems within and after care placements, with a specialized focus on trauma-informed interventions and care.