This study performed comparative analyses in two pediatric cohorts to identify dietary patterns during primary school years and examined their relevance to body composition development. Nutritional and anthropometric data at the beginning of primary school and two or four years later were available from 298 and 372 participants of IDEFICS-Germany (Identification and prevention of Dietary-induced and lifestyle-induced health Effects In Children and infants Study) and the KOPS (Kiel Obesity Prevention Study) cohort, respectively. Principal component analyses (PCA) and reduced rank regression (RRR) were used to identify dietary patterns at baseline and patterns of change in food group intake during primary school years. RRR extracted patterns explaining variations in changes in body mass index (BMI), fat mass index (FMI), and waist-to-height-ratio (WtHR). Associations between pattern adherence and excess gain in BMI, FMI, or WtHR (>75th percentile) during primary school years were examined using logistic regression. Among PCA patterns, only a change towards a more Mediterranean food choice during primary school years were associated with a favorable body composition development in IDEFICS-Germany (p < 0.05). In KOPS, RRR patterns characterized by a frequent consumption of fast foods or starchy carbohydrate foods were consistently associated with an excess gain in BMI and WtHR (all p < 0.005). In IDEFICS-Germany, excess gain in BMI, FMI, and WtHR were predicted by a frequent consumption of nuts, meat, and pizza at baseline and a decrease in the consumption frequency of protein sources and snack carbohydrates during primary school years (all p < 0.01). The study confirms an adverse impact of fast food consumption on body composition during primary school years. Combinations of protein and carbohydrate sources deserve further investigation.