Children from low-income households and minority families have high cardiometabolic risk. Although breakfast consumption is known to improve cardiometabolic health in children, limited randomized control trials (RCT) have explored this association in low-income and racial/ethnic U.S. minority families. This study conducted secondary analyses from TX Sprouts, a school-based gardening, cooking, and nutrition education RCT, to examine the intervention effect on breakfast consumption and how changes in breakfast consumption impact cardiometabolic risk in predominately low-income, multi-ethnic children. TX Sprouts consisted of 16 schools (8 intervention; 8 control) in greater Austin, TX. A total of 18 lessons were taught, including topics on breakfast consumption benefits and choosing healthy food options at school. Children completed clinical measures (e.g., anthropometrics, body composition via bioelectrical impedance), and the number of breakfast occasions (BO) per week (at home and school) was captured via validated survey at baseline and post-intervention. Post-study—Baseline changes in breakfast consumption were used to categorize students as: maintainers (BO −1 to 1 day/week), decreasers (BO ≤−2 day/week), and increasers (BO ≥2 day/week). Optional fasting blood draws were performed on a subsample. Generalized weighted linear mixed modeling tested differences between intervention and control, with schools as random clusters. Analysis of covariance and linear regression examined changes in breakfast consumption on cardiometabolic outcomes, controlling for age, sex, race/ethnicity, free and reduced-price school meal participation (FRL), school site, breakfast location, physical activity, baseline cardiometabolic measures, and BMI z-score. This study included 1417 children (mean age 9 years; 53% male; 58% Hispanic, 63% FRL; breakfast consumption patterns: 63% maintainers, 16% decreasers, and 21% increasers). There was no intervention effect on changes in breakfast consumption. Compared to decreasers, increasers had an increase in insulin (−0.3 µIU/mL vs. +4.1 µIU/mL; p = 0.01) and a larger increase in HOMA-IR (+0.4 vs. +1.5; p < 0.01). Every one-day increase in breakfast consumption decreased fasting insulin by 0.44 µIU/mL, HOMA-IR by 0.11, and hemoglobin A1c by 0.01% (p ≤ 0.03). Increased breakfast consumption was linked to improved glucose control, suggesting breakfast can mitigate risk in a high-risk population. To better understand underlying mechanisms linking breakfast consumption to improved metabolic health, RCTs focusing on breakfast quality and timing are warranted.