The present study aimed to assess energy intake, nutrient profile and food sources in Spanish children participating in the EsNuPI (“Estudio Nutricional en Población Infantil Española”) study. Plausibility of energy intake and adequacy of nutrient intakes to international recommendations were analyzed in a final sample of 1448 subjects (728 boys and 720 girls) and one group representative of the 1 to <10 years old urban Spanish children (reference sample (n = 707)) who consumed milk and one of the same age who consumed adapted milk over the last year (adapted milk consumers sample (n = 741)) were compared. Both groups completed data of a face-to-face and a telephone 24-h dietary recalls. Both the reference and the adapted milk consumers samples reported an adequate daily energy intake (1503 kcal/day and 1404 kcal/day); and a high contribution to total energy from protein (16.5% and 15.6%) and fat (36.5% and 35.9%). Also, a high percentage of children from both samples were below the lower limit of the recommendations for carbohydrates (47.8% and 39.3%). As the percentage of plausible energy reporters was high for both groups (84.7% and 83.5%, respectively), data for the whole sample were analyzed. Milk and dairy, cereals, meat and derived products, fats and oils, bakery and pastry, fruits and vegetables contributed to about 80% of the total energy intake in both groups. However, the reference sample reported significantly more contribution to energy from cereals, meat and meat products, bakery and pastry and ready to cook/eat foods; meanwhile, the adapted milk consumers sample reported significantly more energy from milk and dairy products, fruits and eggs. Those results suggest that adapted milk consumers have better adherence to the food-based dietary guidelines. Further analyses are warranted to characterize food patterns and the quality of the diet in the EsNuPI study population.