The predictive relationship between muscular strength and endurance and cardio-metabolic health, independent from aerobic fitness, is not clear in disadvantaged Hispanic children. The purpose of this study was to examine the predictive relationship between muscular strength and endurance and clustered cardio-metabolic risk, controlling for aerobic fitness, in Hispanic children from low-income schools. Participants were 320 Hispanic children (Mean age = 10.1 ± 1.1 years; 164 girls, 156 boys) recruited during the 2014–2015 and 2015–2016 academic years from five low-income schools from the state of Utah in the U.S. Muscular strength and endurance was assessed using the push-up and curl-up tests and estimated VO2 Peak was calculated from the Progressive Aerobic Cardiovascular Endurance Run. A clustered metabolic syndrome composite score (MetS) was calculated from cardio-metabolic health measurements consisting of HDL cholesterol, triglycerides, waist circumference, blood glucose, and mean arterial pressure (MAP). Multi-level general linear mixed effects models were used to examine the predictive relationship between muscular strength and endurance and MetS, controlling for the effect of aerobic fitness and the clustering of children within classrooms and schools. Children who were in the middle and upper tertiles for muscular strength and endurance associated with a lower (more favorable) MetS score (middle tertile: β = − 2.59, 95% C.I. [− 4.23, − 0.95], p < 0.05; upper tertile: β = − 1.57, 95% C.I. [− 3.20, − 0.16], p < 0.05). The results suggest that higher levels of muscular strength and endurance relate to lower cardio-metabolic risk, independent of aerobic fitness, in Hispanic children from low-income schools.