Objective: Asylum seekers often experience ethnic discrimination on the flight or in the host country, which may be associated with chronic stress and impaired mental health. Dysregulation of the hypothalamic–pituitary–adrenal axis, a known physiological correlate of chronic stress, can be assessed using hair cortisol concentrations (HCC). The present study aimed to investigate how different forms of perceived ethnic discrimination are associated with mental health outcomes, HCC, and protective factors in asylum seekers living in Germany.