Allostatic load (AL) is an aggregate measure of wear and tear on the body due to the chronic activation of the stress response system. The goal of this study was to examine the association between racially motivated housing discrimination (HD) and AL score within a sample of Indigenous university students. Data for this cross-sectional study were collected from Indigenous adults attending university in a small city in western Canada between 2015 and 2017 (N?=?104; mean age?=?27.8 years). An item adapted from the Experience of Discrimination Scale was to assess racially motivated HD in the past 12 months. AL was measured as a composite of 7 biomarkers assessing neuroendocrine, cardiovascular, metabolic, and immune system function. Bias-corrected and accelerated bootstrapped linear regression models were used to examine associations adjusting for age, income, parenthood, and other situations in which discrimination had been experienced. Indigenous university students who experienced racially motivated HD in the past year (16.8% of the sample) had an average AL score of approximately 4, which was almost double that of their peers who had not. In an adjusted model, racially motivated HD was associated with a 1.5 point increase in AL score. This model explained 35% of the adjusted variance in AL score, of which racially motivated HD explained 24%. These results suggest Indigenous adults who experienced racially motivated HD in the past year had early and more pronounced wear and tear on neuroendocrine, cardiovascular, metabolic, and immune system functioning in young and middle adulthood than Indigenous peers who did not. These findings combine with others to highlight the need for increased efforts to prevent racially motivated HD in urban centers.