The purpose of this study was to compare mental health in adolescents with and without migration background after a semester of remote schooling and almost a year of social distancing in Austria. An online survey, supported by the Austrian Federal Ministry of Education, Science and Research, was conducted from 3rd February to 28th February 2021 measuring well-being (WHO-5), depression (PHQ-9), anxiety (GAD-7), sleep quality (ISI), stress (PSS-10), and disordered eating (EAT-8). A matched-pairs analysis with and without migration background was conducted and was checked with whole sample analysis. From a total of 3052 participants, N = 508 had a migration background (first or second generation) and N = 479 could be matched according to age, gender, region, and education with adolescents without migration background. Matched-pairs analyses showed that migration background is associated with poorer mental health concerning well-being, depression, anxiety, and insomnia scores (all p-values < 0.05). Prevalence of depressive symptoms (64.5% vs. 56.5%), anxiety symptoms (53.5% vs. 46.0%), as well as insomnia (31.9% vs. 21.0%) is higher in adolescents with migration background (all p-values ≤ 0.02). Comparison of the whole sample (N = 3052) confirmed these results. Results suggest that migration status is a risk factor for mental health problems among adolescents during the COVID-19 pandemic and highlight the need to implement easily accessible culture- and language-specific health promotion and prevention strategies.