Low-density lipoprotein cholesterol (LDL-C) and apolipoprotein B (ApoB) are established markers of atherosclerotic cardiovascular disease (ASCVD), but when concentrations are discordant ApoB is the superior predictor. Chronic kidney disease (CKD) is associated with ASCVD, yet the independent role of atherogenic lipoproteins is contentious. Four groups were created based upon high and low levels of ApoB and LDL-C. Continuous and categorical variables were compared across groups, as were adjusted markers of CKD. Logistic regression analysis assessed association(s) with CKD based on the groups. Subjects were categorised by LDL-C and ApoB, using cut-off values of >160 mg/dL and >130 mg/dL, respectively. Those with low LDL-C and high ApoB, compared to those with high LDL-C and high ApoB, had significantly higher body mass index (30.7 vs. 30.1 kg/m2) and waist circumference (106.1 vs. 102.7 cm) and the highest fasting blood glucose (117.5 vs. 112.7 mg/dL), insulin (16.6 vs. 13.1 μU/mL) and homeostatic model assessment of insulin resistance (5.3 vs. 3.7) profiles (all p < 0.001). This group, compared to those with high LDL-C and high ApoB, also had the highest levels of urine albumin (2.3 vs. 2.2 mg/L), log albumin-creatinine ratio (2.2 vs. 2.1 mg/g) and serum uric acid (6.1 vs. 5.6 mg/dL) and the lowest estimated glomerular filtration rate (81.3 vs. 88.4 mL/min/1.73 m2) (all p < 0.001). In expanded logistic regression models, using the low LDL-C and low ApoB group as a reference, those with low LDL-C and high ApoB had the strongest association with CKD, odds ratio (95% CI) 1.12 (1.08–1.16). Discordantly high levels of ApoB are independently associated with increased likelihood of CKD. ApoB remains associated with metabolic dysfunction, regardless of LDL-C.