Discrimination is a fundamental determinant of health and health inequities. However, despite the high prevalence of discrimination exposure, there is limited evidence specific to Indigenous populations on the link between discrimination and health. This study employs a validated measure to quantify experiences of everyday discrimination in a national sample of Aboriginal and Torres Strait Islander (Australia’s Indigenous peoples) adults surveyed from 2018 to 2020 (≥16 years, n = 8108). It quantifies Prevalence Ratios (PRs) and 95% Confidence Intervals (CIs) for wellbeing outcomes by level of discrimination exposure, and tests if associations vary by attribution of discrimination to Indigeneity. Of the participants, 41.5% reported no discrimination, 47.5% low, and 11.0% moderate-high. Discrimination was more commonly reported by younger versus older participants, females versus males, and those living in remote versus urban or regional areas. Discrimination was significantly associated in a dose-response manner, with measures of social and emotional wellbeing, culture and identity, health behaviour, and health outcomes. The strength of the association varied across outcomes, from a 10–20% increased prevalence for some outcomes (e.g., disconnection from culture (PR = 1.08; 95% CI: 1.03, 1.14), and high blood pressure (1.20; 1.09, 1.32)), to a five-fold prevalence of alcohol dependence (4.96; 3.64, 6.76), for those with moderate-high versus no discrimination exposure. The association was of consistent strength and direction whether attributed to Indigeneity or not—with three exceptions. Discrimination is associated with a broad range of poor wellbeing outcomes in this large-scale, national, diverse cohort of Aboriginal and Torres Strait Islander adults. These findings support the vast potential to improve Aboriginal and Torres Strait Islander peoples’ wellbeing, and to reduce Indigenous-non-Indigenous inequities, by reducing exposure to discrimination.