This study assessed the mental health of apprentices during the COVID-19 pandemic in Austria and the effect of gender, migration background, work situation, and work sector. An online survey via REDCap was performed with a sample of 1442 apprentices (female: 53.5%, male: 45.4%, diverse: 1.1%, migration background: 28.4%) from 29 March to 18 May 2021. Indicators of mental health were depression (PHQ-9), anxiety (GAD-7), well-being (WHO-5), disordered eating (EAT-8), and insomnia (ISI-7). There was a high prevalence of clinically relevant depression (cut-offs ≥11 for adolescents, ≥10 for adults: 48.3%), anxiety (cut-offs ≥11 for adolescents, ≥10 for adults: 35.4%), insomnia (cut-off ≥15: 27%), and disordered eating (cut-offs ≥2 for men, ≥3 for women: 50.6%). Linear models revealed that apprentices with female and diverse gender, migration background, and unemployed status showed the poorest scores on all mental health measures (all p-values < 0.05) except disordered eating. These findings emphasize the need for intersectional strategies to reduce and prevent adverse mental health consequences of the COVID-19 pandemic for apprentices.