Obesity is a multifactorial disease and it is related to the occurrence of metabolic syndrome and nonalcoholic fatty liver disease (NAFDL) in youth. This study aimed to investigate the effects of a 12-week multicomponent intervention program in markers of metabolic syndrome and NAFLD in Brazilian overweight/obese low-income school-aged children. This quasi-experimental study comprised overweight/obese school-aged children, aged 7–13 years. The participants were assigned to intervention (n = 17) or control group (n = 18). The multicomponent intervention was developed during 12 weeks, consisting of exercise sessions (twice/week; 1 h), nutritional education sessions (once/month), and parental support (twice/week). The following variables were evaluated: anthropometric measures (height, body weight, waist circumference, percentage of body fat); biochemical assays (total cholesterol (TC), triglycerides-TG, high-density lipoprotein-HDL, glucose, aspartate aminotransferase-AST, alanine aminotransferase-ALT), cardiorespiratory fitness, and maturational stage. A cardiovascular disease (CVD) composite z-scores (percentage of body fat, glucose, AST, ALT, TG, and TC/HDL ratio) was also calculated. General linear models were used for data analysis. Compared to the control group, intervention group participants decreased percentage of body fat (Δ − 0.97; p < 0.001), glucose levels (Δ − 0.15; p = 0.005), ALT (Δ − 2.84; p = 0.021), TC/HDL ratio (Δ − 0.93; p < 0.001), CVD composite score (Δ − 0.97; p < 0.001), and total food intake (Δ − 131.44; p = 0.03), while there was no differences between groups on waist circumference, AST, triglycerides, and CRF. A 12-week multicomponent intervention was effective on decreasing some metabolic syndrome parameters in overweight/obese school-aged children.