Risk factors for estimated glomerular filtration rate (eGFR) decline beyond albuminuria are not fully understood in Indigenous Australians who have a 6-fold risk of end-stage kidney disease. We assessed associations between cardio-metabolic risk factors and eGFR decline according to baseline albuminuria status to identify potential treatment targets. The eGFR Follow-up study is a longitudinal cohort of 520 Indigenous Australians. Linear mixed regression was used to estimate associations between baseline cardio-metabolic risk factors and annual Chronic Kidney Disease Epidemiology Collaboration (CKD-EPI) eGFR change (ml/min/1.73 m2 /year), among those classified with baseline normoalbuminuria (uACR <3 mg/mmol; n = 297), microalbuminuria (uACR 3-30 mg/mmol; n = 114) and macroalbuminuria (uACR ≥30 mg/mmol; n = 109). After a median of 3.0 years of follow-up, progressive declines of the age- and sex-adjusted mean eGFR was observed across albuminuria categories (-2.0 [-2.6 to-1.4], -2.5 [-3.7 to -1.3] and -6.3 [-7.8 to -4.9] ml/min/1.72 m2 /year). Although a borderline association was observed between greater baseline HbA1c and eGFR decline in those with macroalbuminuria (p = 0.059), relationships were not significant in those with microalbuminuria (p = 0.187) or normoalbuminuria (p = 0.23). Greater baseline blood pressure, C-reactive protein, waist-to-hip ratio and lower HDL cholesterol showed non-significant trends with greater eGFR decline in the presence of albuminuria. This study demonstrated that in a three year period marked eGFR decline was observed with greater baseline albuminuria. Cardio-metabolic risk factors were not strong predictors for eGFR decline in Indigenous Australians without albuminuria. Longer follow-up may elucidate the role of these predictors and other mechanisms in CKD progression in this population.