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There is limited evidence about the inflammatory potential of diet in children. The aim of this study was to evaluate the association between the Children’s Dietary Inflammatory Index (C-DII) from 5 to 11 years with adiposity and inflammatory biomarkers in Mexican children. We analyzed 726 children from a birth cohort study with complete dietary information and measurements to evaluate adiposity at 5, 7 and 11 y and 286 children with IL-6, hsCRP, leptin and adiponectin information at 11 y. C-DII trajectories were estimated using latent class linear mixed models. We used linear mixed models for adiposity and logistic and multinomial regression for biomarkers. In girls, each one-point increase in C-DII score was associated with greater adiposity (abdominal-circumference 0.41%, <i>p</i> = 0.03; skinfold-sum 1.76%, <i>p</i> = 0.01; and BMI Z-score 0.05, <i>p</i> = 0.01). At 11 y the C-DII was associated with greater leptin (34% ≥ 13.0 ng/mL, <i>p</i> = 0.03) and hsCRP concentrations (29% ≥ 3.00 mg/L, <i>p</i> = 0.06) and lower adiponectin/leptin ratio (75% < 2.45, <i>p</i> = 0.02). C-DII trajectory 3 in boys was associated with a 75.2% (<i>p</i> < 0.01) increase in leptin concentrations and a 37.9% decrease (<i>p</i> = 0.02) in the adiponectin/leptin ratio. This study suggests that the inflammatory potential of diet may influence adiposity in girls and the homeostasis of adipose tissue and chronic subclinical inflammation in 11-year-old children.